├── inst ├── ProbePkg-template │ ├── data │ │ └── .gitignore │ ├── NAMESPACE │ ├── R │ │ └── zzz.R │ ├── DESCRIPTION │ └── man │ │ └── @PKGNAME@.Rd ├── AnnDbPkg-templates │ ├── GO.DB │ │ ├── inst │ │ │ └── extdata │ │ │ │ └── .gitignore │ │ ├── DESCRIPTION │ │ ├── NAMESPACE │ │ ├── man │ │ │ ├── SYNONYM.Rd │ │ │ ├── BASE.Rd │ │ │ └── OBSOLETE.Rd │ │ └── R │ │ │ └── zzz.R │ ├── BASEPKG.DB │ │ ├── inst │ │ │ └── extdata │ │ │ │ └── .gitignore │ │ ├── NAMESPACE │ │ ├── DESCRIPTION │ │ └── man │ │ │ └── BASE.Rd │ ├── KEGG.DB │ │ ├── inst │ │ │ └── extdata │ │ │ │ └── .gitignore │ │ ├── LICENSE │ │ ├── DESCRIPTION │ │ ├── NAMESPACE │ │ ├── R │ │ │ └── zzz.R │ │ └── man │ │ │ ├── PATHID2NAME.Rd │ │ │ ├── PATHNAME2ID.Rd │ │ │ ├── GO2ENZYMEID.Rd │ │ │ ├── ENZYMEID2GO.Rd │ │ │ └── BASE.Rd │ ├── MALARIA.DB │ │ ├── inst │ │ │ └── extdata │ │ │ │ └── .gitignore │ │ ├── NAMESPACE │ │ ├── DESCRIPTION │ │ ├── tests │ │ │ ├── runalltests.R │ │ │ └── unit │ │ │ │ └── test.R │ │ └── man │ │ │ ├── ORGANISM.Rd │ │ │ ├── BASE.Rd │ │ │ └── GENENAME.Rd │ ├── NCBIORG.DB │ │ ├── inst │ │ │ └── extdata │ │ │ │ └── .gitignore │ │ ├── NAMESPACE │ │ ├── DESCRIPTION │ │ ├── man │ │ │ ├── PFAM.Rd │ │ │ ├── PROSITE.Rd │ │ │ ├── ORGANISM.Rd │ │ │ ├── CHRLENGTHS.Rd │ │ │ ├── CHR.Rd │ │ │ ├── BASE.Rd │ │ │ ├── ZFIN.Rd │ │ │ ├── WORMBASE.Rd │ │ │ ├── UNIPROT.Rd │ │ │ ├── GENENAME.Rd │ │ │ ├── MGI.Rd │ │ │ └── FLYBASE.Rd │ │ └── tests │ │ │ ├── runalltests.R │ │ │ └── unit │ │ │ └── test.R │ ├── PFAM.DB │ │ ├── inst │ │ │ └── extdata │ │ │ │ └── .gitignore │ │ ├── NAMESPACE │ │ ├── DESCRIPTION │ │ ├── R │ │ │ └── zzz.R │ │ └── man │ │ │ ├── BASE.Rd │ │ │ └── SCOP2AC.Rd │ ├── YEAST.DB │ │ ├── inst │ │ │ └── extdata │ │ │ │ └── .gitignore │ │ ├── NAMESPACE │ │ ├── DESCRIPTION │ │ ├── tests │ │ │ ├── runalltests.R │ │ │ └── unit │ │ │ │ └── test.R │ │ └── man │ │ │ ├── ORGANISM.Rd │ │ │ ├── CHRLENGTHS.Rd │ │ │ ├── INTERPRO.Rd │ │ │ ├── REJECTORF.Rd │ │ │ ├── SMART.Rd │ │ │ ├── CHR.Rd │ │ │ ├── SGD.Rd │ │ │ ├── BASE.Rd │ │ │ ├── COMMON2ORF.Rd │ │ │ ├── UNIPROT.Rd │ │ │ ├── ENTREZID.Rd │ │ │ ├── ALIAS.Rd │ │ │ ├── GENENAME.Rd │ │ │ └── DESCRIPTION.Rd │ ├── ARABIDOPSIS.DB │ │ ├── inst │ │ │ └── extdata │ │ │ │ └── .gitignore │ │ ├── NAMESPACE │ │ ├── DESCRIPTION │ │ ├── tests │ │ │ ├── runalltests.R │ │ │ └── unit │ │ │ │ └── test.R │ │ └── man │ │ │ ├── ORGANISM.Rd │ │ │ ├── CHRLENGTHS.Rd │ │ │ ├── BASE.Rd │ │ │ ├── ENTREZID.Rd │ │ │ ├── ARACYC.Rd │ │ │ ├── ARACYCENZYME.Rd │ │ │ ├── CHR.Rd │ │ │ ├── GENENAME.Rd │ │ │ └── SYMBOL.Rd │ ├── COELICOLOR.DB │ │ ├── inst │ │ │ └── extdata │ │ │ │ └── .gitignore │ │ ├── NAMESPACE │ │ ├── tests │ │ │ ├── runalltests.R │ │ │ └── unit │ │ │ │ └── test.R │ │ ├── DESCRIPTION │ │ └── man │ │ │ ├── ORGANISM.Rd │ │ │ ├── CHRLENGTHS.Rd │ │ │ ├── CHR.Rd │ │ │ ├── PROTEINGI.Rd │ │ │ ├── LOCUSTAG.Rd │ │ │ ├── BASE.Rd │ │ │ ├── GENENAME.Rd │ │ │ └── ACCNUM.Rd │ ├── INPARANOID.DB │ │ ├── inst │ │ │ └── extdata │ │ │ │ └── .gitignore │ │ ├── DESCRIPTION │ │ ├── NAMESPACE │ │ └── man │ │ │ ├── ORGANISM.Rd │ │ │ └── BASE.Rd │ ├── NCBICHIP.DB │ │ ├── inst │ │ │ └── extdata │ │ │ │ └── .gitignore │ │ ├── NAMESPACE │ │ ├── tests │ │ │ ├── runalltests.R │ │ │ ├── unit │ │ │ │ └── test.R │ │ │ └── runalltests.Rout.save │ │ ├── man │ │ │ ├── PFAM.Rd │ │ │ ├── PROSITE.Rd │ │ │ ├── MAPCOUNTS.Rd │ │ │ ├── CHRLENGTHS.Rd │ │ │ ├── BASE.Rd │ │ │ ├── ZFIN.Rd │ │ │ ├── WORMBASE.Rd │ │ │ ├── UNIPROT.Rd │ │ │ ├── ACCNUM.Rd │ │ │ ├── CHR.Rd │ │ │ ├── FLYBASE.Rd │ │ │ ├── GENENAME.Rd │ │ │ ├── MGI.Rd │ │ │ └── ALIAS2PROBE.Rd │ │ └── DESCRIPTION │ ├── NOCHIPSCHEMA.DB │ │ ├── inst │ │ │ └── extdata │ │ │ │ └── .gitignore │ │ ├── NAMESPACE │ │ ├── DESCRIPTION │ │ ├── man │ │ │ ├── BASE.Rd │ │ │ └── ORGANISM.Rd │ │ └── R │ │ │ └── zzz.R │ ├── NOSCHEMA.DB │ │ ├── inst │ │ │ └── extdata │ │ │ │ └── .gitignore │ │ ├── NAMESPACE │ │ ├── DESCRIPTION │ │ ├── man │ │ │ ├── BASE.Rd │ │ │ └── ORGANISM.Rd │ │ └── R │ │ │ └── zzz.R │ ├── ORGANISM.DB │ │ ├── inst │ │ │ └── extdata │ │ │ │ └── .gitignore │ │ ├── NAMESPACE │ │ ├── DESCRIPTION │ │ ├── tests │ │ │ ├── runalltests.R │ │ │ └── unit │ │ │ │ └── test.R │ │ └── man │ │ │ ├── ORGANISM.Rd │ │ │ ├── CHR.Rd │ │ │ ├── BASE.Rd │ │ │ ├── ACCNUM.Rd │ │ │ └── GENENAME.Rd │ ├── ORTHOLOGY.DB │ │ ├── inst │ │ │ └── extdata │ │ │ │ └── .gitignore │ │ ├── NAMESPACE │ │ ├── DESCRIPTION │ │ ├── tests │ │ │ ├── runalltests.R │ │ │ └── unit │ │ │ │ └── test.R │ │ └── R │ │ │ └── zzz.R │ ├── YEASTCHIP.DB │ │ ├── inst │ │ │ └── extdata │ │ │ │ └── .gitignore │ │ ├── NAMESPACE │ │ ├── tests │ │ │ ├── runalltests.R │ │ │ ├── unit │ │ │ │ └── test.R │ │ │ └── runalltests.Rout.save │ │ ├── DESCRIPTION │ │ └── man │ │ │ ├── MAPCOUNTS.Rd │ │ │ ├── CHRLENGTHS.Rd │ │ │ ├── BASE.Rd │ │ │ ├── CHR.Rd │ │ │ ├── ALIAS.Rd │ │ │ ├── ORF.Rd │ │ │ ├── GENENAME.Rd │ │ │ └── DESCRIPTION.Rd │ ├── YEASTNCBI.DB │ │ ├── inst │ │ │ └── extdata │ │ │ │ └── .gitignore │ │ ├── NAMESPACE │ │ ├── DESCRIPTION │ │ ├── tests │ │ │ ├── runalltests.R │ │ │ └── unit │ │ │ │ └── test.R │ │ └── man │ │ │ ├── ORGANISM.Rd │ │ │ ├── CHRLENGTHS.Rd │ │ │ ├── CHR.Rd │ │ │ ├── BASE.Rd │ │ │ ├── UNIPROT.Rd │ │ │ ├── ORF.Rd │ │ │ ├── SGD.Rd │ │ │ └── GENENAME.Rd │ └── ARABIDOPSISCHIP.DB │ │ ├── inst │ │ └── extdata │ │ │ └── .gitignore │ │ ├── NAMESPACE │ │ ├── tests │ │ ├── runalltests.R │ │ ├── unit │ │ │ └── test.R │ │ └── runalltests.Rout.save │ │ ├── DESCRIPTION │ │ └── man │ │ ├── MAPCOUNTS.Rd │ │ ├── CHRLENGTHS.Rd │ │ ├── BASE.Rd │ │ ├── ORGANISM.Rd │ │ ├── ARACYC.Rd │ │ ├── ARACYCENZYME.Rd │ │ ├── CHR.Rd │ │ └── GENENAME.Rd ├── extdata │ ├── viableIDs.rda │ ├── HG-U95Av2_probe_tab.gz │ ├── inp8_metadata │ └── GentlemanLab │ │ └── org-batch-script.R ├── seqnames-template │ ├── NAMESPACE │ ├── inst │ │ └── extdata │ │ │ └── dataFiles │ │ │ ├── Arabidopsis_thaliana.csv │ │ │ ├── Caenorhabditis_elegans.csv │ │ │ ├── Zea_mays.csv │ │ │ ├── Oryza_sativa.csv │ │ │ ├── Populus_trichocarpa.csv │ │ │ ├── Cyanidioschyzon_merolae.csv │ │ │ ├── Homo_sapiens.csv │ │ │ ├── Drosophila_melanogaster.csv │ │ │ └── Saccharomyces_cerevisiae.csv │ └── DESCRIPTION └── TODO ├── R └── test_AnnotationForge_package.R ├── vignettes ├── Homo_sapiens.pdf └── references.bib ├── tests └── AnnotationForge_unit_tests.R ├── README.md ├── man ├── sqlForge-wrapDBPackages.Rd └── makeInpDb.Rd └── NAMESPACE /inst/ProbePkg-template/data/.gitignore: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/GO.DB/inst/extdata/.gitignore: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/BASEPKG.DB/inst/extdata/.gitignore: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/KEGG.DB/inst/extdata/.gitignore: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/MALARIA.DB/inst/extdata/.gitignore: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/NCBIORG.DB/inst/extdata/.gitignore: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/PFAM.DB/inst/extdata/.gitignore: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/YEAST.DB/inst/extdata/.gitignore: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/ARABIDOPSIS.DB/inst/extdata/.gitignore: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/COELICOLOR.DB/inst/extdata/.gitignore: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/INPARANOID.DB/inst/extdata/.gitignore: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/NCBICHIP.DB/inst/extdata/.gitignore: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/NOCHIPSCHEMA.DB/inst/extdata/.gitignore: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/NOSCHEMA.DB/inst/extdata/.gitignore: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/ORGANISM.DB/inst/extdata/.gitignore: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/ORTHOLOGY.DB/inst/extdata/.gitignore: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/YEASTCHIP.DB/inst/extdata/.gitignore: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/YEASTNCBI.DB/inst/extdata/.gitignore: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/ARABIDOPSISCHIP.DB/inst/extdata/.gitignore: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /R/test_AnnotationForge_package.R: -------------------------------------------------------------------------------- 1 | .test <- function() BiocGenerics:::testPackage("AnnotationForge") 2 | -------------------------------------------------------------------------------- /inst/extdata/viableIDs.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/AnnotationForge/devel/inst/extdata/viableIDs.rda -------------------------------------------------------------------------------- /vignettes/Homo_sapiens.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/AnnotationForge/devel/vignettes/Homo_sapiens.pdf -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/KEGG.DB/LICENSE: -------------------------------------------------------------------------------- 1 | Free for academic use. Non-academic users are requested to obtain a license agreement with KEGG. -------------------------------------------------------------------------------- /inst/extdata/HG-U95Av2_probe_tab.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/AnnotationForge/devel/inst/extdata/HG-U95Av2_probe_tab.gz -------------------------------------------------------------------------------- /inst/seqnames-template/NAMESPACE: -------------------------------------------------------------------------------- 1 | # A NAMESPACE is strictly required by R 2.14 or higher. 2 | # Export everything 3 | exportPattern(".") 4 | -------------------------------------------------------------------------------- /inst/seqnames-template/inst/extdata/dataFiles/Arabidopsis_thaliana.csv: -------------------------------------------------------------------------------- 1 | NCBI TAIR10 2 | 1 1 3 | 2 2 4 | 3 3 5 | 4 4 6 | 5 5 7 | MT Mt 8 | Pltd Pt 9 | -------------------------------------------------------------------------------- /tests/AnnotationForge_unit_tests.R: -------------------------------------------------------------------------------- 1 | require("AnnotationForge") || stop("unable to load AnnotationForge package") 2 | AnnotationForge:::.test() 3 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/BASEPKG.DB/NAMESPACE: -------------------------------------------------------------------------------- 1 | # A NAMESPACE is strictly required by R 2.14 or higher. 2 | # Export everything 3 | exportPattern(".") 4 | -------------------------------------------------------------------------------- /inst/ProbePkg-template/NAMESPACE: -------------------------------------------------------------------------------- 1 | # A NAMESPACE is strictly required by R 2.14 or higher. 2 | # Export everything 3 | exportPattern(".") 4 | importFrom(utils, data) 5 | import(AnnotationDbi) 6 | -------------------------------------------------------------------------------- /vignettes/references.bib: -------------------------------------------------------------------------------- 1 | @article{Rfoundation1999, 2 | title = {Writing R Extensions}, 3 | author = {{R Foundation}}, 4 | year = {1999}, 5 | url = {http://www.r-project.org} 6 | } 7 | -------------------------------------------------------------------------------- /inst/seqnames-template/inst/extdata/dataFiles/Caenorhabditis_elegans.csv: -------------------------------------------------------------------------------- 1 | NCBI UCSC Ensembl 2 | I chrI I 3 | II chrII II 4 | III chrIII III 5 | IV chrIV IV 6 | V chrV V 7 | X chrX X 8 | MT chrM MtDNA 9 | -------------------------------------------------------------------------------- /inst/ProbePkg-template/R/zzz.R: -------------------------------------------------------------------------------- 1 | .onLoad <- function(libname, pkgname) { 2 | ## load the utils::data 3 | where = asNamespace(pkgname) 4 | utils::data(list = pkgname, package = pkgname, envir = where) 5 | } 6 | -------------------------------------------------------------------------------- /inst/seqnames-template/inst/extdata/dataFiles/Zea_mays.csv: -------------------------------------------------------------------------------- 1 | NCBI AGPv2 2 | 1 1 3 | 2 2 4 | 3 3 5 | 4 4 6 | 5 5 7 | 6 6 8 | 7 7 9 | 8 8 10 | 9 9 11 | 10 10 12 | MT mitochondrion 13 | Pltd chloroplast 14 | -------------------------------------------------------------------------------- /inst/seqnames-template/inst/extdata/dataFiles/Oryza_sativa.csv: -------------------------------------------------------------------------------- 1 | NCBI MSU6 2 | 1 1 3 | 2 2 4 | 3 3 5 | 4 4 6 | 5 5 7 | 6 6 8 | 7 7 9 | 8 8 10 | 9 9 11 | 10 10 12 | 11 11 13 | 12 12 14 | MT Mt 15 | Pltd Pt 16 | NA Sy 17 | NA Un 18 | -------------------------------------------------------------------------------- /inst/extdata/inp8_metadata: -------------------------------------------------------------------------------- 1 | name value 2 | INPSOURCEDATE 12-Dec-2013 3 | INPSOURCENAME Inparanoid Orthologs 4 | INPSOURCEURL http://inparanoid.sbc.su.se/download/current/Orthologs/ 5 | DBSCHEMA INPARANOID_DB8 6 | ORGANISM NULL 7 | SPECIES NULL 8 | package AnnotationDbi 9 | Db type Inparanoid8Db 10 | DBSCHEMAVERSION 1.0 11 | -------------------------------------------------------------------------------- /inst/seqnames-template/inst/extdata/dataFiles/Populus_trichocarpa.csv: -------------------------------------------------------------------------------- 1 | NCBI JGI2.0 2 | LGI 1 3 | LGII 2 4 | LGIII 3 5 | LGIV 4 6 | LGV 5 7 | LGVI 6 8 | LGVII 7 9 | LGVIII 8 10 | LGIX 9 11 | LGX 10 12 | LGXI 11 13 | LGXII 12 14 | LGXIII 13 15 | LGIV 14 16 | LGXV 15 17 | LGVI 16 18 | LGVII 17 19 | LGVIII 18 20 | LGXIX 19 21 | Pltd NA 22 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/GO.DB/DESCRIPTION: -------------------------------------------------------------------------------- 1 | Package: @PKGNAME@ 2 | Title: @PKGTITLE@ 3 | Description: @PKGTITLE@ assembled using data from GO 4 | Version: @PKGVERSION@ 5 | Author: @AUTHOR@ 6 | Maintainer: @MAINTAINER@ 7 | Depends: R (>= 2.7.0), methods, AnnotationDbi (>= @ANNDBIVERSION@) 8 | Suggests: DBI 9 | License: @LIC@ 10 | biocViews: @BIOCVIEWS@ 11 | -------------------------------------------------------------------------------- /inst/seqnames-template/inst/extdata/dataFiles/Cyanidioschyzon_merolae.csv: -------------------------------------------------------------------------------- 1 | NCBI ASM9120v1 2 | 1 Chr1 3 | 2 Chr2 4 | 3 Chr3 5 | 4 Chr4 6 | 5 Chr5 7 | 6 Chr6 8 | 7 Chr7 9 | 8 Chr8 10 | 9 Chr9 11 | 10 Chr10 12 | 11 Chr11 13 | 12 Chr12 14 | 13 Chr13 15 | 14 Chr14 16 | 15 Chr15 17 | 16 Chr16 18 | 17 Chr17 19 | 18 Chr18 20 | 19 Chr19 21 | 20 Chr20 22 | MT Mito 23 | Pltd Chloro 24 | -------------------------------------------------------------------------------- /inst/seqnames-template/inst/extdata/dataFiles/Homo_sapiens.csv: -------------------------------------------------------------------------------- 1 | NCBI UCSC 2 | 1 chr1 3 | 2 chr2 4 | 3 chr3 5 | 4 chr4 6 | 5 chr5 7 | 6 chr6 8 | 7 chr7 9 | 8 chr8 10 | 9 chr9 11 | 10 chr10 12 | 11 chr11 13 | 12 chr12 14 | 13 chr13 15 | 14 chr14 16 | 15 chr15 17 | 16 chr16 18 | 17 chr17 19 | 18 chr18 20 | 19 chr19 21 | 20 chr20 22 | 21 chr21 23 | 22 chr22 24 | X chrX 25 | Y chrY 26 | MT chrM 27 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/KEGG.DB/DESCRIPTION: -------------------------------------------------------------------------------- 1 | Package: @PKGNAME@ 2 | Title: @PKGTITLE@ 3 | Description: @PKGTITLE@ assembled using data from KEGG 4 | Version: @PKGVERSION@ 5 | Author: @AUTHOR@ 6 | Maintainer: @MAINTAINER@ 7 | Depends: R (>= 2.7.0), methods, AnnotationDbi (>= @ANNDBIVERSION@) 8 | Suggests: DBI 9 | License: file LICENSE 10 | License_restricts_use: yes 11 | biocViews: @BIOCVIEWS@ 12 | 13 | -------------------------------------------------------------------------------- /inst/seqnames-template/inst/extdata/dataFiles/Drosophila_melanogaster.csv: -------------------------------------------------------------------------------- 1 | NCBI UCSC Ensembl 2 | 2L chr2L 2L 3 | 2R chr2R 2R 4 | 3L chr3L 3L 5 | 3R chr3R 3R 6 | 4 chr4 4 7 | X chrX X 8 | MT chrM dmel_mitochondrion_genome 9 | 2LHet chr2LHet 2LHet 10 | 2Rhet chr2RHet 2RHet 11 | 3LHet chr3LHet 3LHet 12 | 3RHet chr3RHet 3RHet 13 | Xhet chrXHet XHet 14 | Yhet chrYHet YHet 15 | Un chrU U 16 | NA chrUextra Uextra 17 | -------------------------------------------------------------------------------- /inst/seqnames-template/inst/extdata/dataFiles/Saccharomyces_cerevisiae.csv: -------------------------------------------------------------------------------- 1 | NCBI UCSC Ensembl 2 | I chrI I 3 | II chrII II 4 | III chrIII III 5 | IV chrIV IV 6 | V chrV V 7 | VI chrVI VI 8 | VII chrVII VII 9 | VIII chrVIII VIII 10 | IX chrIX IX 11 | X chrX X 12 | XI chrXI XI 13 | XII chrXII XII 14 | XIII chrXIII XIII 15 | XIV chrXIV XIV 16 | XV chrXV XV 17 | XVI chrXVI XVI 18 | MT chrM Mito 19 | 2uM 2micron NA 20 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/ORTHOLOGY.DB/NAMESPACE: -------------------------------------------------------------------------------- 1 | import(methods) 2 | import(AnnotationDbi) 3 | 4 | ### Only put what is statically exported here. All the AnnObj instances 5 | ### created at load time are dynamically exported (refer to R/zzz.R for 6 | ### the details). 7 | export( 8 | @ANNOBJPREFIX@_dbconn, 9 | @ANNOBJPREFIX@_dbfile, 10 | @ANNOBJPREFIX@_dbschema, 11 | @ANNOBJPREFIX@_dbInfo 12 | ) 13 | 14 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/GO.DB/NAMESPACE: -------------------------------------------------------------------------------- 1 | import(methods) 2 | import(AnnotationDbi) 3 | 4 | ### Only put what is statically exported here. All the AnnObj instances 5 | ### created at load time are dynamically exported (refer to R/zzz.R for 6 | ### the details). 7 | export( 8 | @ANNOBJPREFIX@, 9 | @ANNOBJPREFIX@_dbconn, 10 | @ANNOBJPREFIX@_dbfile, 11 | @ANNOBJPREFIX@_dbschema, 12 | @ANNOBJPREFIX@_dbInfo 13 | ) 14 | 15 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/KEGG.DB/NAMESPACE: -------------------------------------------------------------------------------- 1 | import(methods) 2 | import(AnnotationDbi) 3 | 4 | ### Only put what is statically exported here. All the AnnObj instances 5 | ### created at load time are dynamically exported (refer to R/zzz.R for 6 | ### the details). 7 | export( 8 | @ANNOBJPREFIX@, 9 | @ANNOBJPREFIX@_dbconn, 10 | @ANNOBJPREFIX@_dbfile, 11 | @ANNOBJPREFIX@_dbschema, 12 | @ANNOBJPREFIX@_dbInfo 13 | ) 14 | 15 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/PFAM.DB/NAMESPACE: -------------------------------------------------------------------------------- 1 | import(methods) 2 | import(AnnotationDbi) 3 | 4 | ### Only put what is statically exported here. All the AnnObj instances 5 | ### created at load time are dynamically exported (refer to R/zzz.R for 6 | ### the details). 7 | export( 8 | @ANNOBJPREFIX@, 9 | @ANNOBJPREFIX@_dbconn, 10 | @ANNOBJPREFIX@_dbfile, 11 | @ANNOBJPREFIX@_dbschema, 12 | @ANNOBJPREFIX@_dbInfo 13 | ) 14 | 15 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/ORTHOLOGY.DB/DESCRIPTION: -------------------------------------------------------------------------------- 1 | Package: @PKGNAME@ 2 | Title: Orthology mapping package 3 | Description: Orthology mapping package, based on data from NCBI, using NCBI Gene IDs and Taxonomy IDs. 4 | Version: @PKGVERSION@ 5 | Author: @AUTHOR@ 6 | Maintainer: @MAINTAINER@ 7 | Depends: R (>= 2.7.0), methods, AnnotationDbi (>= @ANNDBIVERSION@) 8 | Suggests: DBI, annotate, RUnit 9 | License: @LIC@ 10 | biocViews: OrthologyDb, @BIOCVIEWS@ 11 | 12 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | [](https://bioconductor.org/) 2 | 3 | **AnnotationForge** is an R/Bioconductor package that provides tools for building SQLite-based annotation data packages. 4 | 5 | See https://bioconductor.org/packages/AnnotationForge for more information including how to install the release version of the package (please refrain from installing directly from GitHub). 6 | 7 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/YEAST.DB/NAMESPACE: -------------------------------------------------------------------------------- 1 | import(methods) 2 | import(AnnotationDbi) 3 | 4 | ### Only put what is statically exported here. All the AnnObj instances 5 | ### created at load time are dynamically exported (refer to R/zzz.R for 6 | ### the details). 7 | export( 8 | @ANNOBJPREFIX@, 9 | @ANNOBJPREFIX@_dbconn, 10 | @ANNOBJPREFIX@_dbfile, 11 | @ANNOBJPREFIX@_dbschema, 12 | @ANNOBJPREFIX@_dbInfo, 13 | 14 | @ANNOBJPREFIX@ORGANISM 15 | ) 16 | 17 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/COELICOLOR.DB/NAMESPACE: -------------------------------------------------------------------------------- 1 | import(methods) 2 | import(AnnotationDbi) 3 | 4 | ### Only put what is statically exported here. All the AnnObj instances 5 | ### created at load time are dynamically exported (refer to R/zzz.R for 6 | ### the details). 7 | export( 8 | @ANNOBJPREFIX@, 9 | @ANNOBJPREFIX@_dbconn, 10 | @ANNOBJPREFIX@_dbfile, 11 | @ANNOBJPREFIX@_dbschema, 12 | @ANNOBJPREFIX@_dbInfo, 13 | 14 | @ANNOBJPREFIX@ORGANISM 15 | ) 16 | 17 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/INPARANOID.DB/DESCRIPTION: -------------------------------------------------------------------------------- 1 | Package: @PKGNAME@ 2 | Title: @PKGTITLE@ 3 | Description: @PKGTITLE@ assembled using data from public repositories 4 | Version: @PKGVERSION@ 5 | Encoding: UTF-8 6 | Author: Marc Carlson, Hervé Pagès 7 | Maintainer: @MAINTAINER@ 8 | Depends: R (>= 2.7.0), methods, AnnotationDbi (>= @ANNDBIVERSION@) 9 | Suggests: DBI 10 | License: @LIC@ 11 | organism: @ORGANISM@ 12 | species: @SPECIES@ 13 | biocViews: InparanoidDb, @BIOCVIEWS@ 14 | 15 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/INPARANOID.DB/NAMESPACE: -------------------------------------------------------------------------------- 1 | import(methods) 2 | import(AnnotationDbi) 3 | 4 | ### Only put what is statically exported here. All the AnnObj instances 5 | ### created at load time are dynamically exported (refer to R/zzz.R for 6 | ### the details). 7 | export( 8 | @ANNOBJPREFIX@, 9 | @ANNOBJPREFIX@_dbconn, 10 | @ANNOBJPREFIX@_dbfile, 11 | @ANNOBJPREFIX@_dbschema, 12 | @ANNOBJPREFIX@_dbInfo, 13 | 14 | @ANNOBJPREFIX@ORGANISM 15 | ) 16 | 17 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/MALARIA.DB/NAMESPACE: -------------------------------------------------------------------------------- 1 | import(methods) 2 | import(AnnotationDbi) 3 | 4 | ### Only put what is statically exported here. All the AnnObj instances 5 | ### created at load time are dynamically exported (refer to R/zzz.R for 6 | ### the details). 7 | export( 8 | @ANNOBJPREFIX@, 9 | @ANNOBJPREFIX@_dbconn, 10 | @ANNOBJPREFIX@_dbfile, 11 | @ANNOBJPREFIX@_dbschema, 12 | @ANNOBJPREFIX@_dbInfo, 13 | 14 | @ANNOBJPREFIX@ORGANISM 15 | ) 16 | 17 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/NCBICHIP.DB/NAMESPACE: -------------------------------------------------------------------------------- 1 | import(methods) 2 | import(AnnotationDbi) 3 | 4 | ### Only put what is statically exported here. All the AnnObj instances 5 | ### created at load time are dynamically exported (refer to R/zzz.R for 6 | ### the details). 7 | export( 8 | @ANNOBJPREFIX@, 9 | @ANNOBJPREFIX@_dbconn, 10 | @ANNOBJPREFIX@_dbfile, 11 | @ANNOBJPREFIX@_dbschema, 12 | @ANNOBJPREFIX@_dbInfo, 13 | 14 | @ANNOBJPREFIX@ORGANISM 15 | ) 16 | 17 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/NCBIORG.DB/NAMESPACE: -------------------------------------------------------------------------------- 1 | import(methods) 2 | import(AnnotationDbi) 3 | 4 | ### Only put what is statically exported here. All the AnnObj instances 5 | ### created at load time are dynamically exported (refer to R/zzz.R for 6 | ### the details). 7 | export( 8 | @ANNOBJPREFIX@, 9 | @ANNOBJPREFIX@_dbconn, 10 | @ANNOBJPREFIX@_dbfile, 11 | @ANNOBJPREFIX@_dbschema, 12 | @ANNOBJPREFIX@_dbInfo, 13 | 14 | @ANNOBJPREFIX@ORGANISM 15 | ) 16 | 17 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/NOSCHEMA.DB/NAMESPACE: -------------------------------------------------------------------------------- 1 | import(methods) 2 | import(AnnotationDbi) 3 | 4 | ### Only put what is statically exported here. All the AnnObj instances 5 | ### created at load time are dynamically exported (refer to R/zzz.R for 6 | ### the details). 7 | export( 8 | @ANNOBJPREFIX@, 9 | @ANNOBJPREFIX@_dbconn, 10 | @ANNOBJPREFIX@_dbfile, 11 | @ANNOBJPREFIX@_dbschema, 12 | @ANNOBJPREFIX@_dbInfo, 13 | 14 | @ANNOBJPREFIX@ORGANISM 15 | ) 16 | 17 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/ORGANISM.DB/NAMESPACE: -------------------------------------------------------------------------------- 1 | import(methods) 2 | import(AnnotationDbi) 3 | 4 | ### Only put what is statically exported here. All the AnnObj instances 5 | ### created at load time are dynamically exported (refer to R/zzz.R for 6 | ### the details). 7 | export( 8 | @ANNOBJPREFIX@, 9 | @ANNOBJPREFIX@_dbconn, 10 | @ANNOBJPREFIX@_dbfile, 11 | @ANNOBJPREFIX@_dbschema, 12 | @ANNOBJPREFIX@_dbInfo, 13 | 14 | @ANNOBJPREFIX@ORGANISM 15 | ) 16 | 17 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/YEASTCHIP.DB/NAMESPACE: -------------------------------------------------------------------------------- 1 | import(methods) 2 | import(AnnotationDbi) 3 | 4 | ### Only put what is statically exported here. All the AnnObj instances 5 | ### created at load time are dynamically exported (refer to R/zzz.R for 6 | ### the details). 7 | export( 8 | @ANNOBJPREFIX@, 9 | @ANNOBJPREFIX@_dbconn, 10 | @ANNOBJPREFIX@_dbfile, 11 | @ANNOBJPREFIX@_dbschema, 12 | @ANNOBJPREFIX@_dbInfo, 13 | 14 | @ANNOBJPREFIX@ORGANISM 15 | ) 16 | 17 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/YEASTNCBI.DB/NAMESPACE: -------------------------------------------------------------------------------- 1 | import(methods) 2 | import(AnnotationDbi) 3 | 4 | ### Only put what is statically exported here. All the AnnObj instances 5 | ### created at load time are dynamically exported (refer to R/zzz.R for 6 | ### the details). 7 | export( 8 | @ANNOBJPREFIX@, 9 | @ANNOBJPREFIX@_dbconn, 10 | @ANNOBJPREFIX@_dbfile, 11 | @ANNOBJPREFIX@_dbschema, 12 | @ANNOBJPREFIX@_dbInfo, 13 | 14 | @ANNOBJPREFIX@ORGANISM 15 | ) 16 | 17 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/ARABIDOPSIS.DB/NAMESPACE: -------------------------------------------------------------------------------- 1 | import(methods) 2 | import(AnnotationDbi) 3 | 4 | ### Only put what is statically exported here. All the AnnObj instances 5 | ### created at load time are dynamically exported (refer to R/zzz.R for 6 | ### the details). 7 | export( 8 | @ANNOBJPREFIX@, 9 | @ANNOBJPREFIX@_dbconn, 10 | @ANNOBJPREFIX@_dbfile, 11 | @ANNOBJPREFIX@_dbschema, 12 | @ANNOBJPREFIX@_dbInfo, 13 | 14 | @ANNOBJPREFIX@ORGANISM 15 | ) 16 | 17 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/ARABIDOPSISCHIP.DB/NAMESPACE: -------------------------------------------------------------------------------- 1 | import(methods) 2 | import(AnnotationDbi) 3 | 4 | ### Only put what is statically exported here. All the AnnObj instances 5 | ### created at load time are dynamically exported (refer to R/zzz.R for 6 | ### the details). 7 | export( 8 | @ANNOBJPREFIX@, 9 | @ANNOBJPREFIX@_dbconn, 10 | @ANNOBJPREFIX@_dbfile, 11 | @ANNOBJPREFIX@_dbschema, 12 | @ANNOBJPREFIX@_dbInfo, 13 | 14 | @ANNOBJPREFIX@ORGANISM 15 | ) 16 | 17 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/PFAM.DB/DESCRIPTION: -------------------------------------------------------------------------------- 1 | Package: @PKGNAME@ 2 | Title: @PKGTITLE@ 3 | Description: @PKGTITLE@ assembled using data from public repositories 4 | Version: @PKGVERSION@ 5 | Author: Marc Carlson, Ting-Yuan Liu, ChenWei Lin, Seth Falcon, Jianhua 6 | Zhang, James W. MacDonald 7 | Maintainer: @MAINTAINER@ 8 | Depends: R (>= 2.7.0), methods, AnnotationDbi (>= @ANNDBIVERSION@) 9 | Suggests: DBI 10 | License: @LIC@ 11 | manufacturerUrl: @MANUFURL@ 12 | biocViews: @BIOCVIEWS@ 13 | 14 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/ARABIDOPSIS.DB/DESCRIPTION: -------------------------------------------------------------------------------- 1 | Package: @PKGNAME@ 2 | Title: Genome wide annotation for @SPECIES@ 3 | Description: Genome wide annotation for @SPECIES@, primarily based on mapping using TAIR identifiers. 4 | Version: @PKGVERSION@ 5 | Author: @AUTHOR@ 6 | Maintainer: @MAINTAINER@ 7 | Depends: R (>= 2.7.0), methods, AnnotationDbi (>= @ANNDBIVERSION@) 8 | Suggests: DBI, annotate, RUnit 9 | License: @LIC@ 10 | organism: @ORGANISM@ 11 | species: @SPECIES@ 12 | biocViews: OrgDb, @BIOCVIEWS@ 13 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/NCBICHIP.DB/tests/runalltests.R: -------------------------------------------------------------------------------- 1 | suppressMessages(library("RUnit")) 2 | 3 | options(warn=1) 4 | 5 | dirs <- 'unit' 6 | 7 | testFilePat <- ".*test\\.R$" 8 | 9 | allSuite <- defineTestSuite(name="allSuite", 10 | dirs=dirs, 11 | testFileRegexp=testFilePat, 12 | rngKind="default", 13 | rngNormalKind="default") 14 | 15 | runTestSuite(allSuite) 16 | 17 | q(runLast=FALSE) 18 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/YEASTCHIP.DB/tests/runalltests.R: -------------------------------------------------------------------------------- 1 | suppressMessages(library("RUnit")) 2 | 3 | options(warn=1) 4 | 5 | dirs <- 'unit' 6 | 7 | testFilePat <- ".*test\\.R$" 8 | 9 | allSuite <- defineTestSuite(name="allSuite", 10 | dirs=dirs, 11 | testFileRegexp=testFilePat, 12 | rngKind="default", 13 | rngNormalKind="default") 14 | 15 | runTestSuite(allSuite) 16 | 17 | q(runLast=FALSE) 18 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/BASEPKG.DB/DESCRIPTION: -------------------------------------------------------------------------------- 1 | Package: @PKGNAME@ 2 | Title: Base Level Annotation databases for @SPECIES@ 3 | Description: Base annotation databases for @SPECIES@, intended ONLY to be used by AnnotationDbi to produce regular annotation packages. 4 | Version: @PKGVERSION@ 5 | Author: @AUTHOR@ 6 | Maintainer: @MAINTAINER@ 7 | Depends: R (>= 2.7.0), methods, AnnotationDbi (>= @ANNDBIVERSION@) 8 | License: @LIC@ 9 | organism: @ORGANISM@ 10 | species: @SPECIES@ 11 | biocViews: db0, @BIOCVIEWS@ 12 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/ARABIDOPSISCHIP.DB/tests/runalltests.R: -------------------------------------------------------------------------------- 1 | suppressMessages(library("RUnit")) 2 | 3 | options(warn=1) 4 | 5 | dirs <- 'unit' 6 | 7 | testFilePat <- ".*test\\.R$" 8 | 9 | allSuite <- defineTestSuite(name="allSuite", 10 | dirs=dirs, 11 | testFileRegexp=testFilePat, 12 | rngKind="default", 13 | rngNormalKind="default") 14 | 15 | runTestSuite(allSuite) 16 | 17 | q(runLast=FALSE) 18 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/MALARIA.DB/DESCRIPTION: -------------------------------------------------------------------------------- 1 | Package: @PKGNAME@ 2 | Title: Genome wide annotation for @SPECIES@ 3 | Description: Genome wide annotation for @SPECIES@, primarily based on mapping using Entrez Gene identifiers. 4 | Version: @PKGVERSION@ 5 | Author: @AUTHOR@ 6 | Maintainer: @MAINTAINER@ 7 | Depends: R (>= 2.7.0), methods, AnnotationDbi (>= @ANNDBIVERSION@) 8 | Suggests: DBI, annotate, RUnit 9 | License: @LIC@ 10 | organism: @ORGANISM@ 11 | species: @SPECIES@ 12 | biocViews: OrgDb, @BIOCVIEWS@ 13 | 14 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/NCBIORG.DB/DESCRIPTION: -------------------------------------------------------------------------------- 1 | Package: @PKGNAME@ 2 | Title: Genome wide annotation for @SPECIES@ 3 | Description: Genome wide annotation for @SPECIES@, primarily based on mapping using Entrez Gene identifiers. 4 | Version: @PKGVERSION@ 5 | Author: @AUTHOR@ 6 | Maintainer: @MAINTAINER@ 7 | Depends: R (>= 2.7.0), methods, AnnotationDbi (>= @ANNDBIVERSION@) 8 | Suggests: DBI, annotate, RUnit 9 | License: @LIC@ 10 | organism: @ORGANISM@ 11 | species: @SPECIES@ 12 | biocViews: OrgDb, @BIOCVIEWS@ 13 | 14 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/NOCHIPSCHEMA.DB/NAMESPACE: -------------------------------------------------------------------------------- 1 | import(methods) 2 | import(AnnotationDbi) 3 | 4 | ### Only put what is statically exported here. All the AnnObj instances 5 | ### created at load time are dynamically exported (refer to R/zzz.R for 6 | ### the details). 7 | export( 8 | @ANNOBJPREFIX@, 9 | @ANNOBJPREFIX@_dbconn, 10 | @ANNOBJPREFIX@_dbfile, 11 | @ANNOBJPREFIX@_dbschema, 12 | @ANNOBJPREFIX@_dbInfo, 13 | 14 | @ANNOBJPREFIX@ORGPKG, 15 | @ANNOBJPREFIX@ORGANISM 16 | ) 17 | 18 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/NOSCHEMA.DB/DESCRIPTION: -------------------------------------------------------------------------------- 1 | Package: @PKGNAME@ 2 | Title: Genome wide annotation for @SPECIES@ 3 | Description: Genome wide annotation for @SPECIES@, primarily based on mapping using Entrez Gene identifiers. 4 | Version: @PKGVERSION@ 5 | Author: @AUTHOR@ 6 | Maintainer: @MAINTAINER@ 7 | Depends: R (>= 2.7.0), methods, AnnotationDbi (>= @ANNDBIVERSION@) 8 | Suggests: DBI, annotate, RUnit 9 | License: @LIC@ 10 | organism: @ORGANISM@ 11 | species: @SPECIES@ 12 | biocViews: OrgDb, @BIOCVIEWS@ 13 | 14 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/YEAST.DB/DESCRIPTION: -------------------------------------------------------------------------------- 1 | Package: @PKGNAME@ 2 | Title: Genome wide annotation for @SPECIES@ 3 | Description: Genome wide annotation for @SPECIES@, primarily based on mapping using ORF identifiers from SGD. 4 | Version: @PKGVERSION@ 5 | Author: @AUTHOR@ 6 | Maintainer: @MAINTAINER@ 7 | Depends: R (>= 2.7.0), methods, AnnotationDbi (>= @ANNDBIVERSION@) 8 | Suggests: DBI, annotate, RUnit 9 | License: @LIC@ 10 | organism: @ORGANISM@ 11 | species: @SPECIES@ 12 | biocViews: OrgDb, @BIOCVIEWS@ 13 | 14 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/NCBICHIP.DB/man/PFAM.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@PFAM} 2 | \alias{@ANNOBJPREFIX@PFAM} 3 | \title{Maps between Manufacturer Identifiers and PFAM Identifiers} 4 | \description{ 5 | @ANNOBJPREFIX@PFAM is an R object that provides mappings between 6 | manufacturer identifiers and PFAM identifiers. 7 | } 8 | 9 | \details{ 10 | The bimap interface for PFAM is defunct. Please use select() interface to 11 | PFAM identifiers. See ?AnnotationDbi::select for details. 12 | } 13 | 14 | \keyword{datasets} 15 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/NCBIORG.DB/man/PFAM.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@PFAM} 2 | \alias{@ANNOBJPREFIX@PFAM} 3 | \title{Maps between Manufacturer Identifiers and PFAM Identifiers} 4 | \description{ 5 | @ANNOBJPREFIX@PFAM is an R object that provides mappings between 6 | manufacturer identifiers and PFAM identifiers. 7 | } 8 | 9 | \details{ 10 | The bimap interface for PFAM is defunct. Please use select() interface to 11 | PFAM identifiers. See ?AnnotationDbi::select for details. 12 | } 13 | 14 | \keyword{datasets} 15 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/NOCHIPSCHEMA.DB/DESCRIPTION: -------------------------------------------------------------------------------- 1 | Package: @PKGNAME@ 2 | Title: Chip style package for @SPECIES@ 3 | Description: A custom made chip style package to match probes to gene information for @SPECIES@. 4 | Version: @PKGVERSION@ 5 | Author: @AUTHOR@ 6 | Maintainer: @MAINTAINER@ 7 | Depends: R (>= 2.7.0), methods, AnnotationDbi (>= @ANNDBIVERSION@), @ORGPKGDEP@.db 8 | Suggests: DBI, annotate, RUnit 9 | License: @LIC@ 10 | organism: @ORGANISM@ 11 | species: @SPECIES@ 12 | biocViews: ChipDb, @BIOCVIEWS@ 13 | 14 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/ORGANISM.DB/DESCRIPTION: -------------------------------------------------------------------------------- 1 | Package: @PKGNAME@ 2 | Title: Genome wide annotation for @SPECIES@ 3 | Description: Genome wide annotation for @SPECIES@, primarily based on mapping using Entrez Gene identifiers. 4 | Version: @PKGVERSION@ 5 | Author: @AUTHOR@ 6 | Maintainer: @MAINTAINER@ 7 | Depends: R (>= 2.7.0), methods, AnnotationDbi (>= @ANNDBIVERSION@) 8 | Suggests: DBI,, annotate, RUnit 9 | License: @LIC@ 10 | organism: @ORGANISM@ 11 | species: @SPECIES@ 12 | biocViews: OrgDb, @BIOCVIEWS@ 13 | 14 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/YEASTNCBI.DB/DESCRIPTION: -------------------------------------------------------------------------------- 1 | Package: @PKGNAME@ 2 | Title: Genome wide annotation for @SPECIES@ 3 | Description: Genome wide annotation for @SPECIES@, primarily based on mapping using Entrez Gene identifiers. 4 | Version: @PKGVERSION@ 5 | Author: @AUTHOR@ 6 | Maintainer: @MAINTAINER@ 7 | Depends: R (>= 2.7.0), methods, AnnotationDbi (>= @ANNDBIVERSION@) 8 | Suggests: DBI, annotate, RUnit 9 | License: @LIC@ 10 | organism: @ORGANISM@ 11 | species: @SPECIES@ 12 | biocViews: OrgDb, @BIOCVIEWS@ 13 | 14 | -------------------------------------------------------------------------------- /inst/ProbePkg-template/DESCRIPTION: -------------------------------------------------------------------------------- 1 | Package: @PKGNAME@ 2 | Title: Probe sequence data for microarrays of type @ARRAYTYPE@ 3 | Version: @VERSION@ 4 | Created: @TODAY@ 5 | Author: The Bioconductor Project www.bioconductor.org 6 | Description: This package was automatically created by @CREATOR@. @DATASOURCE@ 7 | Maintainer: @MAINTAINER@ 8 | Depends: R (>= 1.6), AnnotationDbi (>= @ANNOTATIONDBIVERSION@) 9 | Imports: utils 10 | License: LGPL 11 | biocViews: AnnotationData, AffymetrixChip, probe, @ARRAYTYPE@, @SPECIES@ 12 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/MALARIA.DB/tests/runalltests.R: -------------------------------------------------------------------------------- 1 | suppressMessages(library("RUnit")) 2 | 3 | options(warn=1) 4 | 5 | dirs <- 'unit' 6 | 7 | testFilePat <- ".*test\\.R$" 8 | 9 | allSuite <- defineTestSuite(name="allSuite", 10 | dirs=dirs, 11 | testFileRegexp=testFilePat, 12 | rngKind="default", 13 | rngNormalKind="default") 14 | 15 | results <- capture.output(runTestSuite(allSuite)) 16 | 17 | q(runLast=FALSE) 18 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/NCBIORG.DB/tests/runalltests.R: -------------------------------------------------------------------------------- 1 | suppressMessages(library("RUnit")) 2 | 3 | options(warn=1) 4 | 5 | dirs <- 'unit' 6 | 7 | testFilePat <- ".*test\\.R$" 8 | 9 | allSuite <- defineTestSuite(name="allSuite", 10 | dirs=dirs, 11 | testFileRegexp=testFilePat, 12 | rngKind="default", 13 | rngNormalKind="default") 14 | 15 | results <- capture.output(runTestSuite(allSuite)) 16 | 17 | q(runLast=FALSE) 18 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/YEAST.DB/tests/runalltests.R: -------------------------------------------------------------------------------- 1 | suppressMessages(library("RUnit")) 2 | 3 | options(warn=1) 4 | 5 | dirs <- 'unit' 6 | 7 | testFilePat <- ".*test\\.R$" 8 | 9 | allSuite <- defineTestSuite(name="allSuite", 10 | dirs=dirs, 11 | testFileRegexp=testFilePat, 12 | rngKind="default", 13 | rngNormalKind="default") 14 | 15 | results <- capture.output(runTestSuite(allSuite)) 16 | 17 | q(runLast=FALSE) 18 | -------------------------------------------------------------------------------- /inst/seqnames-template/DESCRIPTION: -------------------------------------------------------------------------------- 1 | Package: seqnames.db 2 | Title: Chromosome Name translations 3 | Description: Provides translation information for various kinds of chromosome name conventions. 4 | Version: @VERSION@ 5 | Encoding: UTF-8 6 | Author: Marc Carlson, Hervé Pagès 7 | Maintainer: Bioconductor Package Maintainer 8 | Depends: R (>= 2.15.0), methods, AnnotationDbi (>= @ANNOTATIONDBIVERSION@) 9 | Imports: methods, AnnotationDbi 10 | License: Artistic-2.0 11 | biocViews: AnnotationData 12 | 13 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/ARABIDOPSIS.DB/tests/runalltests.R: -------------------------------------------------------------------------------- 1 | suppressMessages(library("RUnit")) 2 | 3 | options(warn=1) 4 | 5 | dirs <- 'unit' 6 | 7 | testFilePat <- ".*test\\.R$" 8 | 9 | allSuite <- defineTestSuite(name="allSuite", 10 | dirs=dirs, 11 | testFileRegexp=testFilePat, 12 | rngKind="default", 13 | rngNormalKind="default") 14 | 15 | results <- capture.output(runTestSuite(allSuite)) 16 | 17 | q(runLast=FALSE) 18 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/COELICOLOR.DB/tests/runalltests.R: -------------------------------------------------------------------------------- 1 | suppressMessages(library("RUnit")) 2 | 3 | options(warn=1) 4 | 5 | dirs <- 'unit' 6 | 7 | testFilePat <- ".*test\\.R$" 8 | 9 | allSuite <- defineTestSuite(name="allSuite", 10 | dirs=dirs, 11 | testFileRegexp=testFilePat, 12 | rngKind="default", 13 | rngNormalKind="default") 14 | 15 | results <- capture.output(runTestSuite(allSuite)) 16 | 17 | q(runLast=FALSE) 18 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/ORGANISM.DB/tests/runalltests.R: -------------------------------------------------------------------------------- 1 | suppressMessages(library("RUnit")) 2 | 3 | options(warn=1) 4 | 5 | dirs <- 'unit' 6 | 7 | testFilePat <- ".*test\\.R$" 8 | 9 | allSuite <- defineTestSuite(name="allSuite", 10 | dirs=dirs, 11 | testFileRegexp=testFilePat, 12 | rngKind="default", 13 | rngNormalKind="default") 14 | 15 | results <- capture.output(runTestSuite(allSuite)) 16 | 17 | q(runLast=FALSE) 18 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/ORTHOLOGY.DB/tests/runalltests.R: -------------------------------------------------------------------------------- 1 | suppressMessages(library("RUnit")) 2 | 3 | options(warn=1) 4 | 5 | dirs <- 'unit' 6 | 7 | testFilePat <- ".*test\\.R$" 8 | 9 | allSuite <- defineTestSuite(name="allSuite", 10 | dirs=dirs, 11 | testFileRegexp=testFilePat, 12 | rngKind="default", 13 | rngNormalKind="default") 14 | 15 | results <- capture.output(runTestSuite(allSuite)) 16 | 17 | q(runLast=FALSE) 18 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/YEASTNCBI.DB/tests/runalltests.R: -------------------------------------------------------------------------------- 1 | suppressMessages(library("RUnit")) 2 | 3 | options(warn=1) 4 | 5 | dirs <- 'unit' 6 | 7 | testFilePat <- ".*test\\.R$" 8 | 9 | allSuite <- defineTestSuite(name="allSuite", 10 | dirs=dirs, 11 | testFileRegexp=testFilePat, 12 | rngKind="default", 13 | rngNormalKind="default") 14 | 15 | results <- capture.output(runTestSuite(allSuite)) 16 | 17 | q(runLast=FALSE) 18 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/NCBICHIP.DB/man/PROSITE.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@PROSITE} 2 | \alias{@ANNOBJPREFIX@PROSITE} 3 | \title{Maps between Manufacturer Identifiers and PROSITE Identifiers} 4 | \description{ 5 | @ANNOBJPREFIX@PROSITE is an R object that provides mappings between 6 | manufacturer identifiers and PROSITE identifiers. 7 | } 8 | 9 | \details{ 10 | The bimap interface for PROSITE is defunct. Please use select() interface to 11 | PROSITE identifiers. See ?AnnotationDbi::select for details. 12 | } 13 | 14 | \keyword{datasets} 15 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/NCBIORG.DB/man/PROSITE.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@PROSITE} 2 | \alias{@ANNOBJPREFIX@PROSITE} 3 | \title{Maps between Manufacturer Identifiers and PROSITE Identifiers} 4 | \description{ 5 | @ANNOBJPREFIX@PROSITE is an R object that provides mappings between 6 | manufacturer identifiers and PROSITE identifiers. 7 | } 8 | 9 | \details{ 10 | The bimap interface for PROSITE is defunct. Please use select() interface to 11 | PROSITE identifiers. See ?AnnotationDbi::select for details. 12 | } 13 | 14 | \keyword{datasets} 15 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/COELICOLOR.DB/DESCRIPTION: -------------------------------------------------------------------------------- 1 | Package: @PKGNAME@ 2 | Title: Genome wide annotation for @SPECIES@ 3 | Description: Genome wide annotation for @SPECIES@, primarily based on mapping using Entrez Gene identifiers. 4 | Version: @PKGVERSION@ 5 | Author: Roxane Legaie 6 | Maintainer: Roxane Legaie 7 | Depends: R (>= 2.7.0), methods, AnnotationDbi (>= @ANNDBIVERSION@) 8 | Suggests: DBI, annotate, RUnit 9 | License: @LIC@ 10 | organism: @ORGANISM@ 11 | species: @SPECIES@ 12 | biocViews: OrgDb, @BIOCVIEWS@ 13 | 14 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/NCBICHIP.DB/DESCRIPTION: -------------------------------------------------------------------------------- 1 | Package: @PKGNAME@ 2 | Title: @PKGTITLE@ 3 | Description: @PKGTITLE@ assembled using data from public repositories 4 | Version: @PKGVERSION@ 5 | Author: @AUTHOR@ 6 | Maintainer: @MAINTAINER@ 7 | Depends: R (>= 2.7.0), methods, AnnotationDbi (>= @ANNDBIVERSION@), @ORGPKGDEP@ (>= @ORGVERSION@) 8 | Suggests: DBI, annotate, RUnit 9 | License: @LIC@ 10 | organism: @ORGANISM@ 11 | species: @SPECIES@ 12 | manufacturer: @MANUF@ 13 | chipName: @CHIPNAME@ 14 | manufacturerUrl: @MANUFURL@ 15 | biocViews: ChipDb, @BIOCVIEWS@ 16 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/ARABIDOPSISCHIP.DB/DESCRIPTION: -------------------------------------------------------------------------------- 1 | Package: @PKGNAME@ 2 | Title: @PKGTITLE@ 3 | Description: @PKGTITLE@ assembled using data from public repositories 4 | Version: @PKGVERSION@ 5 | Author: @AUTHOR@ 6 | Maintainer: @MAINTAINER@ 7 | Depends: R (>= 2.7.0), methods, AnnotationDbi (>= @ANNDBIVERSION@), org.At.tair.db (>= @ORGVERSION@) 8 | Suggests: DBI, annotate, RUnit 9 | License: @LIC@ 10 | organism: @ORGANISM@ 11 | species: @SPECIES@ 12 | manufacturer: @MANUF@ 13 | chipName: @CHIPNAME@ 14 | manufacturerUrl: @MANUFURL@ 15 | biocViews: ChipDb, @BIOCVIEWS@ 16 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/YEASTCHIP.DB/DESCRIPTION: -------------------------------------------------------------------------------- 1 | Package: @PKGNAME@ 2 | Title: @PKGTITLE@ 3 | Description: @PKGTITLE@ assembled using data from public repositories 4 | Version: @PKGVERSION@ 5 | Author: @AUTHOR@ 6 | Maintainer: @MAINTAINER@ 7 | Depends: R (>= 2.7.0), methods, AnnotationDbi (>= @ANNDBIVERSION@), org.Sc.sgd.db (>= @ORGVERSION@) 8 | Suggests: DBI, annotate, RUnit 9 | License: @LIC@ 10 | organism: @ORGANISM@ 11 | species: @SPECIES@ 12 | manufacturer: @MANUF@ 13 | chipName: @CHIPNAME@ 14 | manufacturerUrl: @MANUFURL@ 15 | biocViews: ChipDb, @BIOCVIEWS@ 16 | 17 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/NOSCHEMA.DB/man/BASE.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@.db} 2 | \alias{@ANNOBJPREFIX@.db} 3 | \alias{@ANNOBJPREFIX@} 4 | \title{Bioconductor annotation data package} 5 | \description{ 6 | 7 | Welcome to the @ANNOBJPREFIX@.db annotation Package. This is an 8 | organism specific package. The purpose is to provide detailed 9 | information about the species abbreviated in the second part of the 10 | package name @ANNOBJPREFIX@.db. This package is updated biannually. 11 | 12 | To learn more about this package, users are encouraged to learn about 13 | the select, columns, keys and keytypes methods. These are described 14 | in a walkthrough on the bioconductor website as well as in the manual 15 | pages and vignettes in the AnnotationDbi package. 16 | } 17 | \keyword{datasets} 18 | 19 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/NOCHIPSCHEMA.DB/man/BASE.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@.db} 2 | \alias{@ANNOBJPREFIX@.db} 3 | \alias{@ANNOBJPREFIX@} 4 | \title{Bioconductor annotation data package} 5 | \description{ 6 | 7 | Welcome to the @ANNOBJPREFIX@.db annotation Package. This is an 8 | platform specific package (sometimes called a chip or ChipDb based 9 | package). The purpose is to provide detailed information about the 10 | platform by mapping probes to genes. The platform is usually 11 | abbreviated by the package name @ANNOBJPREFIX@. 12 | 13 | To learn more about this package, users are encouraged to learn about 14 | the select, columns, keys and keytypes methods. These are described 15 | in a walkthrough on the bioconductor website as well as in the manual 16 | pages and vignettes in the AnnotationDbi package. 17 | } 18 | \keyword{datasets} 19 | 20 | -------------------------------------------------------------------------------- /inst/ProbePkg-template/man/@PKGNAME@.Rd: -------------------------------------------------------------------------------- 1 | \name{@PKGNAME@} 2 | \docType{data} 3 | \alias{@PKGNAME@} 4 | \title{Probe sequence for microarrays of type @ARRAYTYPE@.} 5 | \description{This data object was automatically created by the @CREATOR@.} 6 | \usage{data(@PKGNAME@)} 7 | \format{A data frame with @NROW@ rows and @NCOL@ columns, as follows. 8 | \tabular{lll}{ 9 | sequence \tab character \tab probe sequence \cr 10 | x \tab integer \tab x-coordinate on the array \cr 11 | y \tab integer \tab y-coordinate on the array \cr 12 | Probe.Set.Name \tab character \tab Affymetrix Probe Set Name \cr 13 | Probe.Interrogation.Position \tab integer \tab Probe Interrogation Position \cr 14 | Target.Strandedness \tab factor \tab Target Strandedness\cr 15 | }} 16 | 17 | \source{@DATASOURCE@} 18 | 19 | \keyword{datasets} 20 | \examples{ 21 | @PKGNAME@ 22 | as.data.frame(@PKGNAME@[1:3,]) 23 | } 24 | -------------------------------------------------------------------------------- /inst/TODO: -------------------------------------------------------------------------------- 1 | Some todos: 2 | 3 | 1) links, toTable etc need to be better documented 4 | 5 | 2) hgu95av2_dbschema() should not just cat its output across 6 | the screen - it should return something that could be processed 7 | 8 | 3) Put details on the meta data needed for building chip packages 9 | into the vignette 10 | myMeta = c("DBSCHEMA" = "HUMANCHIP_DB", 11 | "ORGANISM" = "Homo sapiens", 12 | "SPECIES" = "Human", 13 | "MANUFACTURER" = "Affymetrix", 14 | "CHIPNAME" = "Affymetrix Human Genome U95 Set Version 2", 15 | "MANUFACTURERURL" = "http:www.affymetrix.com") 16 | 17 | 4) Add a function to the templates for all the classes to make the 18 | datacache available do this before we push out new devel packages in 19 | January. So near to where you see: 20 | @ANNOBJPREFIX@_dbInfo <- function() dbInfo(datacache) 21 | Add something that will produce: 22 | hgu95av2_datacache(), once it has been called. -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/GO.DB/man/SYNONYM.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@SYNONYM} 2 | \alias{@ANNOBJPREFIX@SYNONYM} 3 | \title{Map from GO synonyms to GO terms} 4 | \description{ 5 | @ANNOBJPREFIX@SYNONYM is an R object that provides mapping 6 | from GO synonyms to GO terms 7 | } 8 | 9 | \details{ 10 | [TODO: Put some details here] 11 | } 12 | 13 | \seealso{ 14 | \itemize{ 15 | \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of 16 | the \code{select()} interface. 17 | } 18 | } 19 | 20 | \examples{ 21 | ## select() interface: 22 | ## Objects in this package can be accessed using the select() interface 23 | ## from the AnnotationDbi package. See ?select for details. 24 | 25 | ## Bimap interface: 26 | x <- @ANNOBJPREFIX@SYNONYM 27 | sample(x, 3) 28 | # GO ID "GO:0009435" has a lot of synonyms 29 | @ANNOBJPREFIX@TERM[["GO:0009435"]] 30 | # GO ID "GO:0006736" is a synonym of GO ID "GO:0009435" 31 | GOID(@ANNOBJPREFIX@SYNONYM[["GO:0006736"]]) 32 | } 33 | \keyword{datasets} 34 | 35 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/ORGANISM.DB/man/ORGANISM.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@ORGANISM} 2 | \alias{@ANNOBJPREFIX@ORGANISM} 3 | \title{The Organism for @ANNOBJPREFIX@} 4 | \description{ 5 | @ANNOBJPREFIX@ORGANISM is an R object that contains a single item: a 6 | character string that names the organism for which @ANNOBJPREFIX@ was built. 7 | } 8 | \details{ 9 | Although the package name is suggestive of the organism for which it 10 | was built, @ANNOBJPREFIX@ORGANISM provides a simple way to programmatically 11 | extract the organism name. 12 | } 13 | 14 | \seealso{ 15 | \itemize{ 16 | \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of 17 | the \code{select()} interface. 18 | } 19 | } 20 | 21 | \examples{ 22 | ## select() interface: 23 | ## Objects in this package can be accessed using the select() interface 24 | ## from the AnnotationDbi package. See ?select for details. 25 | 26 | ## Bimap interface: 27 | @ANNOBJPREFIX@ORGANISM 28 | } 29 | 30 | \keyword{datasets} 31 | 32 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/YEAST.DB/man/ORGANISM.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@ORGANISM} 2 | \alias{@ANNOBJPREFIX@ORGANISM} 3 | \title{The Organism for @ANNOBJPREFIX@} 4 | \description{ 5 | @ANNOBJPREFIX@ORGANISM is an R object that contains a single item: a 6 | character string that names the organism for which @ANNOBJPREFIX@ was built. 7 | } 8 | \details{ 9 | Although the package name is suggestive of the organism for which it 10 | was built, @ANNOBJPREFIX@ORGANISM provides a simple way to programmatically 11 | extract the organism name. 12 | } 13 | 14 | \seealso{ 15 | \itemize{ 16 | \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of 17 | the \code{select()} interface. 18 | } 19 | } 20 | 21 | \examples{ 22 | ## select() interface: 23 | ## Objects in this package can be accessed using the select() interface 24 | ## from the AnnotationDbi package. See ?select for details. 25 | 26 | ## Bimap interface: 27 | @ANNOBJPREFIX@ORGANISM 28 | } 29 | 30 | \keyword{datasets} 31 | 32 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/ARABIDOPSIS.DB/man/ORGANISM.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@ORGANISM} 2 | \alias{@ANNOBJPREFIX@ORGANISM} 3 | \title{The Organism for @ANNOBJPREFIX@} 4 | \description{ 5 | @ANNOBJPREFIX@ORGANISM is an R object that contains a single item: a 6 | character string that names the organism for which @ANNOBJPREFIX@ was built. 7 | } 8 | 9 | \details{ 10 | Although the package name is suggestive of the organism for which it 11 | was built, @ANNOBJPREFIX@ORGANISM provides a simple way to programmatically 12 | extract the organism name. 13 | } 14 | 15 | \seealso{ 16 | \itemize{ 17 | \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of 18 | the \code{select()} interface. 19 | } 20 | } 21 | 22 | \examples{ 23 | ## select() interface: 24 | ## Objects in this package can be accessed using the select() interface 25 | ## from the AnnotationDbi package. See ?select for details. 26 | 27 | ## Bimap interface: 28 | @ANNOBJPREFIX@ORGANISM 29 | } 30 | \keyword{datasets} 31 | 32 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/COELICOLOR.DB/man/ORGANISM.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@ORGANISM} 2 | \alias{@ANNOBJPREFIX@ORGANISM} 3 | \title{The Organism for @ANNOBJPREFIX@} 4 | \description{ 5 | @ANNOBJPREFIX@ORGANISM is an R object that contains a single item: a 6 | character string that names the organism for which @ANNOBJPREFIX@ was built. 7 | } 8 | 9 | \details{ 10 | Although the package name is suggestive of the organism for which it 11 | was built, @ANNOBJPREFIX@ORGANISM provides a simple way to programmatically 12 | extract the organism name. 13 | } 14 | 15 | \seealso{ 16 | \itemize{ 17 | \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of 18 | the \code{select()} interface. 19 | } 20 | } 21 | 22 | \examples{ 23 | ## select() interface: 24 | ## Objects in this package can be accessed using the select() interface 25 | ## from the AnnotationDbi package. See ?select for details. 26 | 27 | ## Bimap interface: 28 | @ANNOBJPREFIX@ORGANISM 29 | } 30 | \keyword{datasets} 31 | 32 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/INPARANOID.DB/man/ORGANISM.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@ORGANISM} 2 | \alias{@ANNOBJPREFIX@ORGANISM} 3 | \title{The Organism for @ANNOBJPREFIX@} 4 | \description{ 5 | @ANNOBJPREFIX@ORGANISM is an R object that contains a single item: a 6 | character string that names the organism for which @ANNOBJPREFIX@ was built. 7 | } 8 | 9 | \details{ 10 | Although the package name is suggestive of the organism for which it 11 | was built, @ANNOBJPREFIX@ORGANISM provides a simple way to programmatically 12 | extract the organism name. 13 | } 14 | 15 | \seealso{ 16 | \itemize{ 17 | \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of 18 | the \code{select()} interface. 19 | } 20 | } 21 | 22 | \examples{ 23 | ## select() interface: 24 | ## Objects in this package can be accessed using the select() interface 25 | ## from the AnnotationDbi package. See ?select for details. 26 | 27 | ## Bimap interface: 28 | @ANNOBJPREFIX@ORGANISM 29 | } 30 | \keyword{datasets} 31 | 32 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/MALARIA.DB/man/ORGANISM.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@ORGANISM} 2 | \alias{@ANNOBJPREFIX@ORGANISM} 3 | \title{The Organism for @ANNOBJPREFIX@} 4 | \description{ 5 | @ANNOBJPREFIX@ORGANISM is an R object that contains a single item: a 6 | character string that names the organism for which @ANNOBJPREFIX@ was built. 7 | } 8 | 9 | \details{ 10 | Although the package name is suggestive of the organism for which it 11 | was built, @ANNOBJPREFIX@ORGANISM provides a simple way to programmatically 12 | extract the organism name. 13 | } 14 | 15 | \seealso{ 16 | \itemize{ 17 | \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of 18 | the \code{select()} interface. 19 | } 20 | } 21 | 22 | \examples{ 23 | ## select() interface: 24 | ## Objects in this package can be accessed using the select() interface 25 | ## from the AnnotationDbi package. See ?select for details. 26 | 27 | ## Bimap interface: 28 | @ANNOBJPREFIX@ORGANISM 29 | } 30 | 31 | \keyword{datasets} 32 | 33 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/NCBIORG.DB/man/ORGANISM.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@ORGANISM} 2 | \alias{@ANNOBJPREFIX@ORGANISM} 3 | \title{The Organism for @ANNOBJPREFIX@} 4 | \description{ 5 | @ANNOBJPREFIX@ORGANISM is an R object that contains a single item: a 6 | character string that names the organism for which @ANNOBJPREFIX@ was built. 7 | } 8 | 9 | \details{ 10 | Although the package name is suggestive of the organism for which it 11 | was built, @ANNOBJPREFIX@ORGANISM provides a simple way to programmatically 12 | extract the organism name. 13 | } 14 | 15 | \seealso{ 16 | \itemize{ 17 | \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of 18 | the \code{select()} interface. 19 | } 20 | } 21 | 22 | \examples{ 23 | ## select() interface: 24 | ## Objects in this package can be accessed using the select() interface 25 | ## from the AnnotationDbi package. See ?select for details. 26 | 27 | ## Bimap interface: 28 | @ANNOBJPREFIX@ORGANISM 29 | } 30 | 31 | \keyword{datasets} 32 | 33 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/NOSCHEMA.DB/man/ORGANISM.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@ORGANISM} 2 | \alias{@ANNOBJPREFIX@ORGANISM} 3 | \title{The Organism for @ANNOBJPREFIX@} 4 | \description{ 5 | @ANNOBJPREFIX@ORGANISM is an R object that contains a single item: a 6 | character string that names the organism for which @ANNOBJPREFIX@ was built. 7 | } 8 | 9 | \details{ 10 | Although the package name is suggestive of the organism for which it 11 | was built, @ANNOBJPREFIX@ORGANISM provides a simple way to programmatically 12 | extract the organism name. 13 | } 14 | 15 | \seealso{ 16 | \itemize{ 17 | \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of 18 | the \code{select()} interface. 19 | } 20 | } 21 | 22 | \examples{ 23 | ## select() interface: 24 | ## Objects in this package can be accessed using the select() interface 25 | ## from the AnnotationDbi package. See ?select for details. 26 | 27 | ## Bimap interface: 28 | @ANNOBJPREFIX@ORGANISM 29 | } 30 | 31 | \keyword{datasets} 32 | 33 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/NOCHIPSCHEMA.DB/man/ORGANISM.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@ORGANISM} 2 | \alias{@ANNOBJPREFIX@ORGANISM} 3 | \title{The Organism for @ANNOBJPREFIX@} 4 | \description{ 5 | @ANNOBJPREFIX@ORGANISM is an R object that contains a single item: a 6 | character string that names the organism for which @ANNOBJPREFIX@ was built. 7 | } 8 | 9 | \details{ 10 | Although the package name is suggestive of the organism for which it 11 | was built, @ANNOBJPREFIX@ORGANISM provides a simple way to programmatically 12 | extract the organism name. 13 | } 14 | 15 | \seealso{ 16 | \itemize{ 17 | \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of 18 | the \code{select()} interface. 19 | } 20 | } 21 | 22 | \examples{ 23 | ## select() interface: 24 | ## Objects in this package can be accessed using the select() interface 25 | ## from the AnnotationDbi package. See ?select for details. 26 | 27 | ## Bimap interface: 28 | @ANNOBJPREFIX@ORGANISM 29 | } 30 | 31 | \keyword{datasets} 32 | 33 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/YEASTNCBI.DB/man/ORGANISM.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@ORGANISM} 2 | \alias{@ANNOBJPREFIX@ORGANISM} 3 | \title{The Organism for @ANNOBJPREFIX@} 4 | \description{ 5 | @ANNOBJPREFIX@ORGANISM is an R object that contains a single item: a 6 | character string that names the organism for which @ANNOBJPREFIX@ was built. 7 | } 8 | 9 | \details{ 10 | Although the package name is suggestive of the organism for which it 11 | was built, @ANNOBJPREFIX@ORGANISM provides a simple way to programmatically 12 | extract the organism name. 13 | } 14 | 15 | \seealso{ 16 | \itemize{ 17 | \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of 18 | the \code{select()} interface. 19 | } 20 | } 21 | 22 | \examples{ 23 | ## select() interface: 24 | ## Objects in this package can be accessed using the select() interface 25 | ## from the AnnotationDbi package. See ?select for details. 26 | 27 | ## Bimap interface: 28 | @ANNOBJPREFIX@ORGANISM 29 | } 30 | 31 | \keyword{datasets} 32 | 33 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/NCBICHIP.DB/man/MAPCOUNTS.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@MAPCOUNTS} 2 | 3 | \alias{@ANNOBJPREFIX@MAPCOUNTS} 4 | 5 | 6 | \title{Number of mapped keys for the maps in package @PKGNAME@} 7 | 8 | \description{ 9 | DEPRECATED. Counts in the MAPCOUNT table are out of sync and should 10 | not be used. 11 | 12 | @ANNOBJPREFIX@MAPCOUNTS provides the "map count" (i.e. the 13 | count of mapped keys) for each map in package @PKGNAME@. 14 | } 15 | 16 | \details{ 17 | DEPRECATED. Counts in the MAPCOUNT table are out of sync and should 18 | not be used. 19 | 20 | This "map count" information is precalculated and stored in the 21 | package annotation DB. This allows some quality control and is used by 22 | the \code{\link[AnnotationDbi:AnnDbPkg-checker]{checkMAPCOUNTS}} 23 | function defined in AnnotationDbi to compare and validate different 24 | methods (like \code{count.mappedkeys(x)} or 25 | \code{sum(!is.na(as.list(x)))}) for getting the "map count" of a given 26 | map. 27 | } 28 | 29 | \keyword{datasets} 30 | 31 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/YEASTCHIP.DB/man/MAPCOUNTS.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@MAPCOUNTS} 2 | 3 | \alias{@ANNOBJPREFIX@MAPCOUNTS} 4 | 5 | 6 | \title{Number of mapped keys for the maps in package @PKGNAME@} 7 | 8 | \description{ 9 | DEPRECATED. Counts in the MAPCOUNT table are out of sync and should 10 | not be used. 11 | 12 | @ANNOBJPREFIX@MAPCOUNTS provides the "map count" (i.e. the 13 | count of mapped keys) for each map in package @PKGNAME@. 14 | } 15 | 16 | \details{ 17 | DEPRECATED. Counts in the MAPCOUNT table are out of sync and should 18 | not be used. 19 | 20 | This "map count" information is precalculated and stored in the 21 | package annotation DB. This allows some quality control and is used by 22 | the \code{\link[AnnotationDbi:AnnDbPkg-checker]{checkMAPCOUNTS}} 23 | function defined in AnnotationDbi to compare and validate different 24 | methods (like \code{count.mappedkeys(x)} or 25 | \code{sum(!is.na(as.list(x)))}) for getting the "map count" of a given 26 | map. 27 | } 28 | 29 | \keyword{datasets} 30 | 31 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/ARABIDOPSISCHIP.DB/man/MAPCOUNTS.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@MAPCOUNTS} 2 | 3 | \alias{@ANNOBJPREFIX@MAPCOUNTS} 4 | 5 | 6 | \title{Number of mapped keys for the maps in package @PKGNAME@} 7 | 8 | \description{ 9 | DEPRECATED. Counts in the MAPCOUNT table are out of sync and should 10 | not be used. 11 | 12 | @ANNOBJPREFIX@MAPCOUNTS provides the "map count" (i.e. the 13 | count of mapped keys) for each map in package @PKGNAME@. 14 | } 15 | 16 | \details{ 17 | DEPRECATED. Counts in the MAPCOUNT table are out of sync and should 18 | not be used. 19 | 20 | This "map count" information is precalculated and stored in the 21 | package annotation DB. This allows some quality control and is used by 22 | the \code{\link[AnnotationDbi:AnnDbPkg-checker]{checkMAPCOUNTS}} 23 | function defined in AnnotationDbi to compare and validate different 24 | methods (like \code{count.mappedkeys(x)} or 25 | \code{sum(!is.na(as.list(x)))}) for getting the "map count" of a given 26 | map. 27 | } 28 | 29 | \keyword{datasets} 30 | 31 | -------------------------------------------------------------------------------- /man/sqlForge-wrapDBPackages.Rd: -------------------------------------------------------------------------------- 1 | \name{wrapBaseDBPackages} 2 | \alias{wrapBaseDBPackages} 3 | 4 | \title{Wrap up all the Base Databases into Packages for distribution} 5 | 6 | \description{ 7 | Creates extremely simple packages from the base database files for 8 | distribution. This is a convenience function for wrapping up these 9 | packages in a consistent way each time. 10 | } 11 | 12 | \usage{ 13 | wrapBaseDBPackages(dbPath, destDir, version) 14 | } 15 | 16 | \arguments{ 17 | \item{dbPath}{ 18 | dbPath is just the path to the location of the latest intermediate 19 | sqlite source files. These files are then used to make base DB 20 | packages. 21 | } 22 | \item{destDir}{ 23 | destination path for the newly minted packages. 24 | } 25 | \item{version}{ 26 | version number to stamp onto these newly minted packages. 27 | } 28 | } 29 | 30 | \examples{ 31 | \dontrun{ 32 | ##Make all of the intermediate DBs and place the new packages right here. 33 | wrapBaseDBPackages(dbPath, destDir = ".") 34 | } 35 | } 36 | 37 | \keyword{utilities} 38 | -------------------------------------------------------------------------------- /inst/extdata/GentlemanLab/org-batch-script.R: -------------------------------------------------------------------------------- 1 | ### Wrap all sqlite files found under /mnt/cpb_anno/mcarlson/sanctionedSqlite 2 | ### into a .db package. 3 | 4 | srcdir <- "/mnt/cpb_anno/mcarlson/sanctionedSqlite" 5 | exclude <- c( 6 | "YEAST.sqlite", 7 | "metadatasrc.sqlite", 8 | "megaGO.sqlite", 9 | "chipsrc_arabidopsis.sqlite", 10 | "chipsrc_mouse.sqlite", 11 | "chipsrc_human.sqlite", 12 | "chipsrc_fly.sqlite", 13 | "chipsrc_yeast.sqlite", 14 | "chipsrc_rat.sqlite", 15 | "chipmapsrc_arabidopsis.sqlite", 16 | "chipmapsrc_all.sqlite", 17 | "chipmapsrc_fly.sqlite", 18 | "chipmapsrc_human.sqlite", 19 | "chipmapsrc_mouse.sqlite", 20 | "chipmapsrc_rat.sqlite", 21 | "humanCHRLOC.sqlite", 22 | "mouseCHRLOC.sqlite", 23 | "ratCHRLOC.sqlite", 24 | "flyCHRLOC.sqlite" 25 | ) 26 | 27 | sqlitefiles <- list.files(srcdir, pattern="^org") 28 | sqlitefiles <- sqlitefiles[!(sqlitefiles %in% exclude)] 29 | pkgs <- paste(substr(sqlitefiles, 1, nchar(sqlitefiles)-7), ".db", sep="") 30 | 31 | library(AnnotationForge) 32 | makeAnnDbPkg(pkgs) 33 | 34 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/NCBICHIP.DB/man/CHRLENGTHS.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@CHRLENGTHS} 2 | \alias{@ANNOBJPREFIX@CHRLENGTHS} 3 | \title{A named vector for the length of each of the chromosomes} 4 | \description{ 5 | @ANNOBJPREFIX@CHRLENGTHS provides the length measured in base pairs for 6 | each of the chromosomes. 7 | } 8 | \details{ 9 | This is a named vector with chromosome numbers as the names and the 10 | corresponding lengths for chromosomes as the values. 11 | 12 | Total lengths of chromosomes were derived by calculating the 13 | number of base pairs on the sequence string for each chromosome. 14 | } 15 | 16 | \seealso{ 17 | \itemize{ 18 | \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of 19 | the \code{select()} interface. 20 | } 21 | } 22 | 23 | \examples{ 24 | ## select() interface: 25 | ## Objects in this package can be accessed using the select() interface 26 | ## from the AnnotationDbi package. See ?select for details. 27 | 28 | ## Bimap interface: 29 | tt <- @ANNOBJPREFIX@CHRLENGTHS 30 | # Length of chromosome 1 31 | tt["1"] 32 | } 33 | \keyword{datasets} 34 | 35 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/NCBIORG.DB/man/CHRLENGTHS.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@CHRLENGTHS} 2 | \alias{@ANNOBJPREFIX@CHRLENGTHS} 3 | \title{A named vector for the length of each of the chromosomes} 4 | \description{ 5 | @ANNOBJPREFIX@CHRLENGTHS provides the length measured in base pairs for 6 | each of the chromosomes. 7 | } 8 | \details{ 9 | This is a named vector with chromosome numbers as the names and the 10 | corresponding lengths for chromosomes as the values. 11 | 12 | Total lengths of chromosomes were derived by calculating the 13 | number of base pairs on the sequence string for each chromosome. 14 | } 15 | 16 | \seealso{ 17 | \itemize{ 18 | \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of 19 | the \code{select()} interface. 20 | } 21 | } 22 | 23 | \examples{ 24 | ## select() interface: 25 | ## Objects in this package can be accessed using the select() interface 26 | ## from the AnnotationDbi package. See ?select for details. 27 | 28 | ## Bimap interface: 29 | tt <- @ANNOBJPREFIX@CHRLENGTHS 30 | # Length of chromosome 1 31 | tt["1"] 32 | } 33 | 34 | \keyword{datasets} 35 | 36 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/ARABIDOPSIS.DB/man/CHRLENGTHS.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@CHRLENGTHS} 2 | \alias{@ANNOBJPREFIX@CHRLENGTHS} 3 | \title{A named vector for the length of each of the chromosomes} 4 | \description{ 5 | @ANNOBJPREFIX@CHRLENGTHS provides the length measured in base pairs for 6 | each of the chromosomes. 7 | } 8 | 9 | \details{ 10 | This is a named vector with chromosome numbers as the names and the 11 | corresponding lengths for chromosomes as the values. 12 | 13 | Total lengths of chromosomes were derived by calculating the 14 | number of base pairs on the sequence string for each chromosome. 15 | 16 | } 17 | 18 | \seealso{ 19 | \itemize{ 20 | \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of 21 | the \code{select()} interface. 22 | } 23 | } 24 | 25 | \examples{ 26 | ## select() interface: 27 | ## Objects in this package can be accessed using the select() interface 28 | ## from the AnnotationDbi package. See ?select for details. 29 | 30 | ## Bimap interface: 31 | tt <- @ANNOBJPREFIX@CHRLENGTHS 32 | # Length of chromosome 1 33 | tt["1"] 34 | } 35 | \keyword{datasets} 36 | 37 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/ARABIDOPSISCHIP.DB/man/CHRLENGTHS.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@CHRLENGTHS} 2 | \alias{@ANNOBJPREFIX@CHRLENGTHS} 3 | \title{A named vector for the length of each of the chromosomes} 4 | \description{ 5 | @ANNOBJPREFIX@CHRLENGTHS provides the length measured in base pairs for 6 | each of the chromosomes. 7 | } 8 | \details{ 9 | This is a named vector with chromosome numbers as the names and the 10 | corresponding lengths for chromosomes as the values. 11 | 12 | Total lengths of chromosomes were derived by calculating the 13 | number of base pairs on the sequence string for each chromosome. 14 | 15 | } 16 | 17 | \seealso{ 18 | \itemize{ 19 | \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of 20 | the \code{select()} interface. 21 | } 22 | } 23 | 24 | \examples{ 25 | ## select() interface: 26 | ## Objects in this package can be accessed using the select() interface 27 | ## from the AnnotationDbi package. See ?select for details. 28 | 29 | ## Bimap interface: 30 | tt <- @ANNOBJPREFIX@CHRLENGTHS 31 | # Length of chromosome 1 32 | tt["1"] 33 | } 34 | \keyword{datasets} 35 | 36 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/COELICOLOR.DB/man/CHRLENGTHS.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@CHRLENGTHS} 2 | \alias{@ANNOBJPREFIX@CHRLENGTHS} 3 | \title{A named vector for the length of each of the chromosomes} 4 | \description{ 5 | @ANNOBJPREFIX@CHRLENGTHS provides the length measured in base pairs for 6 | each of the chromosomes. 7 | } 8 | 9 | \details{ 10 | This is a named vector with chromosome numbers as the names and the 11 | corresponding lengths for chromosomes as the values. 12 | 13 | Total lengths of chromosomes were derived by calculating the 14 | number of base pairs on the sequence string for each chromosome. 15 | 16 | } 17 | 18 | \seealso{ 19 | \itemize{ 20 | \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of 21 | the \code{select()} interface. 22 | } 23 | } 24 | 25 | \examples{ 26 | ## select() interface: 27 | ## Objects in this package can be accessed using the select() interface 28 | ## from the AnnotationDbi package. See ?select for details. 29 | 30 | ## Bimap interface: 31 | tt <- @ANNOBJPREFIX@CHRLENGTHS 32 | # Length of chromosome 1 33 | tt["1"] 34 | } 35 | \keyword{datasets} 36 | 37 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/YEAST.DB/man/CHRLENGTHS.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@CHRLENGTHS} 2 | \alias{@ANNOBJPREFIX@CHRLENGTHS} 3 | \title{A named vector for the length of each of the chromosomes} 4 | \description{ 5 | @ANNOBJPREFIX@CHRLENGTHS provides the length measured in base pairs for 6 | each of the chromosomes. 7 | } 8 | \details{ 9 | This is a named vector with chromosome numbers as the names and the 10 | corresponding lengths for chromosomes as the values. 11 | 12 | Total lengths of chromosomes were derived by calculating the 13 | number of base pairs on the sequence string for each chromosome. 14 | 15 | } 16 | 17 | \seealso{ 18 | \itemize{ 19 | \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of 20 | the \code{select()} interface. 21 | } 22 | } 23 | 24 | \examples{ 25 | ## select() interface: 26 | ## Objects in this package can be accessed using the select() interface 27 | ## from the AnnotationDbi package. See ?select for details. 28 | 29 | ## Bimap interface: 30 | tt <- @ANNOBJPREFIX@CHRLENGTHS 31 | # Length of chromosome 1 32 | tt["1"] 33 | } 34 | 35 | \keyword{datasets} 36 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/YEASTCHIP.DB/man/CHRLENGTHS.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@CHRLENGTHS} 2 | \alias{@ANNOBJPREFIX@CHRLENGTHS} 3 | \title{A named vector for the length of each of the chromosomes} 4 | \description{ 5 | @ANNOBJPREFIX@CHRLENGTHS provides the length measured in base pairs for 6 | each of the chromosomes. 7 | } 8 | 9 | \details{ 10 | This is a named vector with chromosome numbers as the names and the 11 | corresponding lengths for chromosomes as the values. 12 | 13 | Total lengths of chromosomes were derived by calculating the 14 | number of base pairs on the sequence string for each chromosome. 15 | } 16 | 17 | \seealso{ 18 | \itemize{ 19 | \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of 20 | the \code{select()} interface. 21 | } 22 | } 23 | 24 | \examples{ 25 | ## select() interface: 26 | ## Objects in this package can be accessed using the select() interface 27 | ## from the AnnotationDbi package. See ?select for details. 28 | 29 | ## Bimap interface: 30 | tt <- @ANNOBJPREFIX@CHRLENGTHS 31 | # Length of chromosome 1 32 | tt["1"] 33 | } 34 | 35 | \keyword{datasets} 36 | 37 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/YEASTNCBI.DB/man/CHRLENGTHS.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@CHRLENGTHS} 2 | \alias{@ANNOBJPREFIX@CHRLENGTHS} 3 | \title{A named vector for the length of each of the chromosomes} 4 | \description{ 5 | @ANNOBJPREFIX@CHRLENGTHS provides the length measured in base pairs for 6 | each of the chromosomes. 7 | } 8 | \details{ 9 | This is a named vector with chromosome numbers as the names and the 10 | corresponding lengths for chromosomes as the values. 11 | 12 | Total lengths of chromosomes were derived by calculating the 13 | number of base pairs on the sequence string for each chromosome. 14 | 15 | } 16 | 17 | \seealso{ 18 | \itemize{ 19 | \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of 20 | the \code{select()} interface. 21 | } 22 | } 23 | 24 | \examples{ 25 | ## select() interface: 26 | ## Objects in this package can be accessed using the select() interface 27 | ## from the AnnotationDbi package. See ?select for details. 28 | 29 | ## Bimap interface: 30 | tt <- @ANNOBJPREFIX@CHRLENGTHS 31 | # Length of chromosome 1 32 | tt["1"] 33 | } 34 | 35 | \keyword{datasets} 36 | 37 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/YEAST.DB/man/INTERPRO.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@INTERPRO} 2 | \alias{@ANNOBJPREFIX@INTERPRO} 3 | \title{Map Yeast Systematic Names to InterPro IDs} 4 | \description{ 5 | @ANNOBJPREFIX@INTERPRO is an R object that provides mappings between yeast 6 | ORF identifiers and the associated InterPro identifiers. 7 | } 8 | \details{ 9 | Each yeast ORF identifier maps to a vector of InterPro identifiers. 10 | 11 | Mappings were based on data provided by: 12 | 13 | @INTERPROSOURCE@ 14 | } 15 | 16 | \references{ 17 | InterPro website: \url{http://www.ebi.ac.uk/interpro/} 18 | } 19 | 20 | \seealso{ 21 | \itemize{ 22 | \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of 23 | the \code{select()} interface. 24 | } 25 | } 26 | 27 | \examples{ 28 | ## select() interface: 29 | ## Objects in this package can be accessed using the select() interface 30 | ## from the AnnotationDbi package. See ?select for details. 31 | 32 | ## Bimap interface: 33 | # Convert to a list 34 | xxx <- as.list(@ANNOBJPREFIX@INTERPRO) 35 | # randomly display 10 probes 36 | sample(xxx, 10) 37 | } 38 | 39 | \keyword{datasets} 40 | 41 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/YEAST.DB/man/REJECTORF.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@REJECTORF} 2 | \alias{@ANNOBJPREFIX@REJECTORF} 3 | \title{Rejected Yeast Genes (ORF)} 4 | \description{ 5 | This is based upon Real and rejected yeast ORFs from Kellis et 6 | al. (2003) to list the rejected genes by this criteria. 7 | } 8 | \details{ 9 | A character vector which contains yeast ORFs which are rejected 10 | in the reading frame conseration (RFC) test in Kellis et al. (2003). 11 | } 12 | 13 | \references{ 14 | Manolis Kellis, Nick Patterson, Matthew Endrizzi, Bruce Birren and 15 | Eric S. Lander, Sequencing and comparison of yeast species to identify 16 | genes and regulatory elements. Nature 423, 241-254 (15 May 2003) 17 | } 18 | 19 | \seealso{ 20 | \itemize{ 21 | \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of 22 | the \code{select()} interface. 23 | } 24 | } 25 | 26 | \examples{ 27 | ## select() interface: 28 | ## Objects in this package can be accessed using the select() interface 29 | ## from the AnnotationDbi package. See ?select for details. 30 | 31 | ## Bimap interface: 32 | head(@ANNOBJPREFIX@REJECTORF) 33 | } 34 | 35 | \keyword{datasets} 36 | 37 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/YEAST.DB/man/SMART.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@SMART} 2 | \alias{@ANNOBJPREFIX@SMART} 3 | \title{Map Yeast ORF Identifiers to SMART IDs} 4 | \description{ 5 | @ANNOBJPREFIX@SMART is an R object that provides mappings between yeast 6 | ORF Identifiers and the associated SMART identifiers. 7 | } 8 | \details{ 9 | Each yeast systematic name maps to a vector of SMART identifiers. 10 | 11 | Mappings were based on data provided by: 12 | 13 | Saccharomyces Genome Database 14 | 15 | Package built on Thu Mar 15 18:04:19 2007 16 | } 17 | \references{ 18 | SMART website: \url{http://smart.embl-heidelberg.de/} 19 | } 20 | 21 | \seealso{ 22 | \itemize{ 23 | \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of 24 | the \code{select()} interface. 25 | } 26 | } 27 | 28 | \examples{ 29 | ## select() interface: 30 | ## Objects in this package can be accessed using the select() interface 31 | ## from the AnnotationDbi package. See ?select for details. 32 | 33 | ## Bimap interface: 34 | # Convert to a list 35 | xxx <- as.list(@ANNOBJPREFIX@SMART) 36 | # randomly display 10 probes 37 | sample(xxx, 10) 38 | } 39 | 40 | \keyword{datasets} 41 | 42 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/KEGG.DB/R/zzz.R: -------------------------------------------------------------------------------- 1 | datacache <- new.env(hash=TRUE, parent=emptyenv()) 2 | 3 | @ANNOBJPREFIX@ <- function() showQCData("@ANNOBJPREFIX@", datacache) 4 | @ANNOBJPREFIX@_dbconn <- function() dbconn(datacache) 5 | @ANNOBJPREFIX@_dbfile <- function() dbfile(datacache) 6 | @ANNOBJPREFIX@_dbschema <- function(file="", show.indices=FALSE) dbschema(datacache, file=file, show.indices=show.indices) 7 | @ANNOBJPREFIX@_dbInfo <- function() dbInfo(datacache) 8 | 9 | .onLoad <- function(libname, pkgname) 10 | { 11 | ## Connect to the SQLite DB 12 | dbfile <- system.file("extdata", "@DBFILE@", package=pkgname, lib.loc=libname) 13 | assign("dbfile", dbfile, envir=datacache) 14 | dbconn <- dbFileConnect(dbfile) 15 | assign("dbconn", dbconn, envir=datacache) 16 | ## Create the AnnObj instances 17 | ann_objs <- createAnnObjs.SchemaChoice("@DBSCHEMA@", "@ANNOBJPREFIX@", "@ANNOBJTARGET@", dbconn, datacache) 18 | mergeToNamespaceAndExport(ann_objs, pkgname) 19 | packageStartupMessage(AnnotationDbi:::annoStartupMessages("@ANNOBJPREFIX@.db")) 20 | } 21 | 22 | .onUnload <- function(libpath) 23 | { 24 | dbFileDisconnect(@ANNOBJPREFIX@_dbconn()) 25 | } 26 | 27 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/PFAM.DB/R/zzz.R: -------------------------------------------------------------------------------- 1 | datacache <- new.env(hash=TRUE, parent=emptyenv()) 2 | 3 | @ANNOBJPREFIX@ <- function() showQCData("@ANNOBJPREFIX@", datacache) 4 | @ANNOBJPREFIX@_dbconn <- function() dbconn(datacache) 5 | @ANNOBJPREFIX@_dbfile <- function() dbfile(datacache) 6 | @ANNOBJPREFIX@_dbschema <- function(file="", show.indices=FALSE) dbschema(datacache, file=file, show.indices=show.indices) 7 | @ANNOBJPREFIX@_dbInfo <- function() dbInfo(datacache) 8 | 9 | .onLoad <- function(libname, pkgname) 10 | { 11 | ## Connect to the SQLite DB 12 | dbfile <- system.file("extdata", "@DBFILE@", package=pkgname, lib.loc=libname) 13 | assign("dbfile", dbfile, envir=datacache) 14 | dbconn <- dbFileConnect(dbfile) 15 | assign("dbconn", dbconn, envir=datacache) 16 | ## Create the AnnObj instances 17 | ann_objs <- createAnnObjs.SchemaChoice("@DBSCHEMA@", "@ANNOBJPREFIX@", "@ANNOBJTARGET@", dbconn, datacache) 18 | mergeToNamespaceAndExport(ann_objs, pkgname) 19 | packageStartupMessage(AnnotationDbi:::annoStartupMessages("@ANNOBJPREFIX@.db")) 20 | } 21 | 22 | .onUnload <- function(libpath) 23 | { 24 | dbFileDisconnect(@ANNOBJPREFIX@_dbconn()) 25 | } 26 | 27 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/YEAST.DB/man/CHR.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@CHR} 2 | \alias{@ANNOBJPREFIX@CHR} 3 | \title{Map ORF IDs to Chromosomes} 4 | \description{ 5 | @ANNOBJPREFIX@CHR is an R object that provides mappings between ORF 6 | identifiers and the chromosome that contains the gene of interest. 7 | } 8 | \details{ 9 | Each ORF identifier maps to a vector of a chromosome. 10 | 11 | Mappings were based on data provided by: @CHRSOURCE@ 12 | } 13 | 14 | \seealso{ 15 | \itemize{ 16 | \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of 17 | the \code{select()} interface. 18 | } 19 | } 20 | 21 | \examples{ 22 | ## select() interface: 23 | ## Objects in this package can be accessed using the select() interface 24 | ## from the AnnotationDbi package. See ?select for details. 25 | 26 | ## Bimap interface: 27 | x <- @ANNOBJPREFIX@CHR 28 | # Get the ORF identifiers that are mapped to a chromosome 29 | mapped_genes <- mappedkeys(x) 30 | # Convert to a list 31 | xx <- as.list(x[mapped_genes]) 32 | if(length(xx) > 0) { 33 | # Get the CHR for the first five genes 34 | xx[1:5] 35 | # Get the first one 36 | xx[[1]] 37 | } 38 | } 39 | \keyword{datasets} 40 | 41 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/NCBICHIP.DB/tests/unit/test.R: -------------------------------------------------------------------------------- 1 | ## verify probes and genes exist (for the chip packages) 2 | library(DBI) 3 | getProbes <- function(){ 4 | require("@PKGNAME@") 5 | as.numeric(dbGetQuery(dbconn(@PKGNAME@), 6 | "SELECT count(DISTINCT probe_id) FROM probes")) 7 | } 8 | 9 | msg = paste("This package has no probes. This can be caused by a large number ", 10 | "of upstream changes. But it's usually caused by alterations to the source ", 11 | "files used to extrac the probes at the very beginning.", sep="") 12 | 13 | checkTrue(getProbes() > 0, 14 | msg = paste(strwrap(msg, exdent=2),collapse="\n") ) 15 | 16 | 17 | getGenes <- function(){ 18 | require("@PKGNAME@") 19 | as.numeric(dbGetQuery(dbconn(@PKGNAME@), 20 | "SELECT count(DISTINCT gene_id) FROM probes")) 21 | } 22 | 23 | msg = paste("This package has no genes. This can be caused by a large number ", 24 | "of upstream changes. But it's usually caused by alterations to the source ", 25 | "files used to extrac the probes at the very beginning.", sep="") 26 | 27 | checkTrue(getGenes() > 0, 28 | msg = paste(strwrap(msg, exdent=2),collapse="\n") ) 29 | 30 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/YEAST.DB/man/SGD.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@SGD} 2 | \alias{@ANNOBJPREFIX@SGD} 3 | \title{Map Systematic ORF identifiers with SGD accession numbers} 4 | \description{ 5 | @ANNOBJPREFIX@SGD is an R object that contains mappings between 6 | Systematic ORF accessions and SGD accession numbers. 7 | } 8 | 9 | \details{ 10 | This object is a simple mapping of Systematic ORF Accession Numbers to 11 | SGD identifiers. 12 | } 13 | 14 | \seealso{ 15 | \itemize{ 16 | \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of 17 | the \code{select()} interface. 18 | } 19 | } 20 | 21 | \examples{ 22 | ## select() interface: 23 | ## Objects in this package can be accessed using the select() interface 24 | ## from the AnnotationDbi package. See ?select for details. 25 | 26 | ## Bimap interface: 27 | x <- @ANNOBJPREFIX@SGD 28 | # Get the Systematic ORF Accessions that are mapped to a SGD ID 29 | mapped_genes <- mappedkeys(x) 30 | # Convert to a list 31 | xx <- as.list(x[mapped_genes]) 32 | if(length(xx) > 0) { 33 | # Get the SGD gene IDs for the first five genes 34 | xx[1:5] 35 | # Get the first one 36 | xx[[1]] 37 | } 38 | } 39 | \keyword{datasets} 40 | 41 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/YEASTCHIP.DB/tests/unit/test.R: -------------------------------------------------------------------------------- 1 | ## verify probes and genes exist (for the chip packages) 2 | library(DBI) 3 | getProbes <- function(){ 4 | require("@PKGNAME@") 5 | as.numeric(dbGetQuery(dbconn(@PKGNAME@), 6 | "SELECT count(DISTINCT probe_id) FROM probes")) 7 | } 8 | 9 | msg = paste("This package has no probes. This can be caused by a large number ", 10 | "of upstream changes. But it's usually caused by alterations to the source ", 11 | "files used to extrac the probes at the very beginning.", sep="") 12 | 13 | checkTrue(getProbes() > 0, 14 | msg = paste(strwrap(msg, exdent=2),collapse="\n") ) 15 | 16 | 17 | getGenes <- function(){ 18 | require("@PKGNAME@") 19 | as.numeric(dbGetQuery(dbconn(@PKGNAME@), 20 | "SELECT count(DISTINCT sgd_id) FROM probes")) 21 | } 22 | 23 | msg = paste("This package has no genes. This can be caused by a large number ", 24 | "of upstream changes. But it's usually caused by alterations to the source ", 25 | "files used to extrac the probes at the very beginning.", sep="") 26 | 27 | checkTrue(getGenes() > 0, 28 | msg = paste(strwrap(msg, exdent=2),collapse="\n") ) 29 | 30 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/ARABIDOPSISCHIP.DB/tests/unit/test.R: -------------------------------------------------------------------------------- 1 | ## verify probes and genes exist (for the chip packages) 2 | library(DBI) 3 | getProbes <- function(){ 4 | require("@PKGNAME@") 5 | as.numeric(dbGetQuery(dbconn(@PKGNAME@), 6 | "SELECT count(DISTINCT probe_id) FROM probes")) 7 | } 8 | 9 | msg = paste("This package has no probes. This can be caused by a large number ", 10 | "of upstream changes. But it's usually caused by alterations to the source ", 11 | "files used to extrac the probes at the very beginning.", sep="") 12 | 13 | checkTrue(getProbes() > 0, 14 | msg = paste(strwrap(msg, exdent=2),collapse="\n") ) 15 | 16 | 17 | getGenes <- function(){ 18 | require("@PKGNAME@") 19 | as.numeric(dbGetQuery(dbconn(@PKGNAME@), 20 | "SELECT count(DISTINCT gene_id) FROM probes")) 21 | } 22 | 23 | msg = paste("This package has no genes. This can be caused by a large number ", 24 | "of upstream changes. But it's usually caused by alterations to the source ", 25 | "files used to extrac the probes at the very beginning.", sep="") 26 | 27 | checkTrue(getGenes() > 0, 28 | msg = paste(strwrap(msg, exdent=2),collapse="\n") ) 29 | 30 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/PFAM.DB/man/BASE.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@.db} 2 | \alias{@ANNOBJPREFIX@.db} 3 | \alias{@ANNOBJPREFIX@} 4 | \title{Bioconductor annotation data package} 5 | \description{ 6 | 7 | Welcome to the @ANNOBJPREFIX@.db annotation Package. The purpose of 8 | this package is to provide detailed information about the 9 | @ANNOBJPREFIX@ platform. This package is updated biannually. 10 | 11 | Objects in this package are accessed using the \code{select()} interface. 12 | See ?select in the AnnotationDbi package for details. 13 | } 14 | 15 | \seealso{ 16 | \itemize{ 17 | \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of 18 | \code{keys()}, \code{columns()} and \code{select()}. 19 | } 20 | } 21 | 22 | \examples{ 23 | ## select() interface: 24 | ## Objects in this package can be accessed using the select() interface 25 | ## from the AnnotationDbi package. See ?select for details. 26 | 27 | ## Bimap interface: 28 | ## The 'old style' of interacting with these objects is manipulation as 29 | ## bimaps. While this approach is still available we strongly encourage the 30 | ## use of select(). 31 | ls("package:@ANNOBJPREFIX@.db") 32 | } 33 | 34 | \keyword{datasets} 35 | 36 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/NCBIORG.DB/man/CHR.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@CHR} 2 | \alias{@ANNOBJPREFIX@CHR} 3 | \title{Map Entrez Gene IDs to Chromosomes} 4 | \description{ 5 | @ANNOBJPREFIX@CHR is an R object that provides mappings between entrez gene 6 | identifiers and the chromosome that contains the gene of interest. 7 | } 8 | \details{ 9 | Each entrez gene identifier maps to a vector of a chromosome. 10 | 11 | Mappings were based on data provided by: @CHRSOURCE@ 12 | } 13 | 14 | \seealso{ 15 | \itemize{ 16 | \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of 17 | the \code{select()} interface. 18 | } 19 | } 20 | 21 | \examples{ 22 | ## select() interface: 23 | ## Objects in this package can be accessed using the select() interface 24 | ## from the AnnotationDbi package. See ?select for details. 25 | 26 | ## Bimap interface: 27 | x <- @ANNOBJPREFIX@CHR 28 | # Get the entrez gene identifiers that are mapped to a chromosome 29 | mapped_genes <- mappedkeys(x) 30 | # Convert to a list 31 | xx <- as.list(x[mapped_genes]) 32 | if(length(xx) > 0) { 33 | # Get the CHR for the first five genes 34 | xx[1:5] 35 | # Get the first one 36 | xx[[1]] 37 | } 38 | } 39 | \keyword{datasets} 40 | 41 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/YEASTNCBI.DB/man/CHR.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@CHR} 2 | \alias{@ANNOBJPREFIX@CHR} 3 | \title{Map Entrez Gene IDs to Chromosomes} 4 | \description{ 5 | @ANNOBJPREFIX@CHR is an R object that provides mappings between entrez gene 6 | identifiers and the chromosome that contains the gene of interest. 7 | } 8 | \details{ 9 | Each entrez gene identifier maps to a vector of a chromosome. 10 | 11 | Mappings were based on data provided by: @CHRSOURCE@ 12 | } 13 | 14 | \seealso{ 15 | \itemize{ 16 | \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of 17 | the \code{select()} interface. 18 | } 19 | } 20 | 21 | \examples{ 22 | ## select() interface: 23 | ## Objects in this package can be accessed using the select() interface 24 | ## from the AnnotationDbi package. See ?select for details. 25 | 26 | ## Bimap interface: 27 | x <- @ANNOBJPREFIX@CHR 28 | # Get the entrez gene identifiers that are mapped to a chromosome 29 | mapped_genes <- mappedkeys(x) 30 | # Convert to a list 31 | xx <- as.list(x[mapped_genes]) 32 | if(length(xx) > 0) { 33 | # Get the CHR for the first five genes 34 | xx[1:5] 35 | # Get the first one 36 | xx[[1]] 37 | } 38 | } 39 | \keyword{datasets} 40 | 41 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/ORGANISM.DB/man/CHR.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@CHR} 2 | \alias{@ANNOBJPREFIX@CHR} 3 | \title{Map Entrez Gene IDs to Chromosomes} 4 | \description{ 5 | @ANNOBJPREFIX@CHR is an R object that provides mappings between entrez gene 6 | identifiers and the chromosome that contains the gene of interest. 7 | } 8 | \details{ 9 | Each entrez gene identifier maps to a vector of a chromosome. 10 | 11 | Mappings were based on data provided by: @CHRSOURCE@ 12 | } 13 | 14 | \seealso{ 15 | \itemize{ 16 | \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of 17 | the \code{select()} interface. 18 | } 19 | } 20 | 21 | \examples{ 22 | ## select() interface: 23 | ## Objects in this package can be accessed using the select() interface 24 | ## from the AnnotationDbi package. See ?select for details. 25 | 26 | ## Bimap interface: 27 | x <- @ANNOBJPREFIX@CHR 28 | # Get the entrez gene identifiers that are mapped to a chromosome 29 | mapped_genes <- mappedkeys(x) 30 | # Convert to a list 31 | xx <- as.list(x[mapped_genes]) 32 | if(length(xx) > 0) { 33 | # Get the CHR for the first five genes 34 | xx[1:5] 35 | # Get the first one 36 | xx[[1]] 37 | } 38 | } 39 | 40 | \keyword{datasets} 41 | 42 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/COELICOLOR.DB/man/CHR.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@CHR} 2 | \alias{@ANNOBJPREFIX@CHR} 3 | \title{Map Entrez Gene IDs to Chromosomes} 4 | \description{ 5 | @ANNOBJPREFIX@CHR is an R object that provides mappings between entrez gene 6 | identifiers and the chromosome that contains the gene of interest. 7 | } 8 | 9 | \details{ 10 | Each entrez gene identifier maps to a vector of a chromosome. 11 | 12 | Mappings were based on data provided by: @CHRSOURCE@ 13 | } 14 | 15 | \seealso{ 16 | \itemize{ 17 | \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of 18 | the \code{select()} interface. 19 | } 20 | } 21 | 22 | \examples{ 23 | ## select() interface: 24 | ## Objects in this package can be accessed using the select() interface 25 | ## from the AnnotationDbi package. See ?select for details. 26 | 27 | ## Bimap interface: 28 | x <- @ANNOBJPREFIX@CHR 29 | # Get the entrez gene identifiers that are mapped to a chromosome 30 | mapped_genes <- mappedkeys(x) 31 | # Convert to a list 32 | xx <- as.list(x[mapped_genes]) 33 | if(length(xx) > 0) { 34 | # Get the CHR for the first five genes 35 | xx[1:5] 36 | # Get the first one 37 | xx[[1]] 38 | } 39 | } 40 | 41 | \keyword{datasets} 42 | 43 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/NCBICHIP.DB/tests/runalltests.Rout.save: -------------------------------------------------------------------------------- 1 | 2 | R version 2.9.0 Under development (unstable) (--) 3 | Copyright (C) The R Foundation for Statistical Computing 4 | ISBN 3-900051-07-0 5 | 6 | R is free software and comes with ABSOLUTELY NO WARRANTY. 7 | You are welcome to redistribute it under certain conditions. 8 | Type 'license()' or 'licence()' for distribution details. 9 | 10 | R is a collaborative project with many contributors. 11 | Type 'contributors()' for more information and 12 | 'citation()' on how to cite R or R packages in publications. 13 | 14 | Type 'demo()' for some demos, 'help()' for on-line help, or 15 | 'help.start()' for an HTML browser interface to help. 16 | Type 'q()' to quit R. 17 | 18 | > suppressMessages(library("RUnit")) 19 | > 20 | > options(warn=1) 21 | > 22 | > dirs <- 'unit' 23 | > 24 | > testFilePat <- ".*test\\.R$" 25 | > 26 | > allSuite <- defineTestSuite(name="allSuite", 27 | + dirs=dirs, 28 | + testFileRegexp=testFilePat, 29 | + rngKind="default", 30 | + rngNormalKind="default") 31 | > 32 | > results <- capture.output(runTestSuite(allSuite)) 33 | > 34 | > q(runLast=FALSE) 35 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/YEASTCHIP.DB/tests/runalltests.Rout.save: -------------------------------------------------------------------------------- 1 | 2 | R version 2.9.0 Under development (unstable) (--) 3 | Copyright (C) The R Foundation for Statistical Computing 4 | ISBN 3-900051-07-0 5 | 6 | R is free software and comes with ABSOLUTELY NO WARRANTY. 7 | You are welcome to redistribute it under certain conditions. 8 | Type 'license()' or 'licence()' for distribution details. 9 | 10 | R is a collaborative project with many contributors. 11 | Type 'contributors()' for more information and 12 | 'citation()' on how to cite R or R packages in publications. 13 | 14 | Type 'demo()' for some demos, 'help()' for on-line help, or 15 | 'help.start()' for an HTML browser interface to help. 16 | Type 'q()' to quit R. 17 | 18 | > suppressMessages(library("RUnit")) 19 | > 20 | > options(warn=1) 21 | > 22 | > dirs <- 'unit' 23 | > 24 | > testFilePat <- ".*test\\.R$" 25 | > 26 | > allSuite <- defineTestSuite(name="allSuite", 27 | + dirs=dirs, 28 | + testFileRegexp=testFilePat, 29 | + rngKind="default", 30 | + rngNormalKind="default") 31 | > 32 | > results <- capture.output(runTestSuite(allSuite)) 33 | > 34 | > q(runLast=FALSE) 35 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/ARABIDOPSIS.DB/man/BASE.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@.db} 2 | \alias{@ANNOBJPREFIX@.db} 3 | \alias{@ANNOBJPREFIX@} 4 | \title{Bioconductor annotation data package} 5 | \description{ 6 | 7 | Welcome to the @ANNOBJPREFIX@.db annotation Package. The purpose of 8 | this package is to provide detailed information about the 9 | @ANNOBJPREFIX@ platform. This package is updated biannually. 10 | 11 | Objects in this package are accessed using the \code{select()} interface. 12 | See ?select in the AnnotationDbi package for details. 13 | } 14 | 15 | \seealso{ 16 | \itemize{ 17 | \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of 18 | \code{keys()}, \code{columns()} and \code{select()}. 19 | } 20 | } 21 | 22 | \examples{ 23 | ## select() interface: 24 | ## Objects in this package can be accessed using the select() interface 25 | ## from the AnnotationDbi package. See ?select for details. 26 | columns(@ANNOBJPREFIX@.db) 27 | 28 | ## Bimap interface: 29 | ## The 'old style' of interacting with these objects is manipulation as 30 | ## bimaps. While this approach is still available we strongly encourage the 31 | ## use of select(). 32 | ls("package:@ANNOBJPREFIX@.db") 33 | } 34 | 35 | \keyword{datasets} 36 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/ARABIDOPSISCHIP.DB/tests/runalltests.Rout.save: -------------------------------------------------------------------------------- 1 | 2 | R version 2.9.0 Under development (unstable) (--) 3 | Copyright (C) The R Foundation for Statistical Computing 4 | ISBN 3-900051-07-0 5 | 6 | R is free software and comes with ABSOLUTELY NO WARRANTY. 7 | You are welcome to redistribute it under certain conditions. 8 | Type 'license()' or 'licence()' for distribution details. 9 | 10 | R is a collaborative project with many contributors. 11 | Type 'contributors()' for more information and 12 | 'citation()' on how to cite R or R packages in publications. 13 | 14 | Type 'demo()' for some demos, 'help()' for on-line help, or 15 | 'help.start()' for an HTML browser interface to help. 16 | Type 'q()' to quit R. 17 | 18 | > suppressMessages(library("RUnit")) 19 | > 20 | > options(warn=1) 21 | > 22 | > dirs <- 'unit' 23 | > 24 | > testFilePat <- ".*test\\.R$" 25 | > 26 | > allSuite <- defineTestSuite(name="allSuite", 27 | + dirs=dirs, 28 | + testFileRegexp=testFilePat, 29 | + rngKind="default", 30 | + rngNormalKind="default") 31 | > 32 | > results <- capture.output(runTestSuite(allSuite)) 33 | > 34 | > q(runLast=FALSE) 35 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/GO.DB/man/BASE.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@.db} 2 | \alias{@ANNOBJPREFIX@.db} 3 | \alias{@ANNOBJPREFIX@} 4 | \title{Bioconductor annotation data package} 5 | \description{ 6 | 7 | Welcome to the @ANNOBJPREFIX@.db annotation Package. The purpose of this 8 | package is to provide detailed information about the latest version of the 9 | Gene Ontologies. This package is updated biannually. 10 | 11 | Objects in this package are accessed using the \code{select()} interface. 12 | See ?select in the AnnotationDbi package for details. 13 | } 14 | 15 | \seealso{ 16 | \itemize{ 17 | \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of 18 | \code{keys()}, \code{columns()} and \code{select()}. 19 | } 20 | } 21 | 22 | \examples{ 23 | ## select() interface: 24 | ## Objects in this package can be accessed using the select() interface 25 | ## from the AnnotationDbi package. See ?select for details. 26 | columns(@ANNOBJPREFIX@.db) 27 | 28 | ## Bimap interface: 29 | ## The 'old style' of interacting with these objects is manipulation as 30 | ## bimaps. While this approach is still available we strongly encourage the 31 | ## use of select(). 32 | ls("package:@ANNOBJPREFIX@.db") 33 | } 34 | \keyword{datasets} 35 | 36 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/NCBICHIP.DB/man/BASE.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@.db} 2 | \alias{@ANNOBJPREFIX@.db} 3 | \alias{@ANNOBJPREFIX@} 4 | \title{Bioconductor annotation data package} 5 | \description{ 6 | 7 | Welcome to the @ANNOBJPREFIX@.db annotation Package. The purpose of 8 | this package is to provide detailed information about the 9 | @ANNOBJPREFIX@ platform. This package is updated biannually. 10 | 11 | Objects in this package are accessed using the \code{select()} interface. 12 | See ?select in the AnnotationDbi package for details. 13 | } 14 | 15 | \seealso{ 16 | \itemize{ 17 | \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of 18 | \code{keys()}, \code{columns()} and \code{select()}. 19 | } 20 | } 21 | 22 | \examples{ 23 | ## select() interface: 24 | ## Objects in this package can be accessed using the select() interface 25 | ## from the AnnotationDbi package. See ?select for details. 26 | columns(@ANNOBJPREFIX@.db) 27 | 28 | ## Bimap interface: 29 | ## The 'old style' of interacting with these objects is manipulation as 30 | ## bimaps. While this approach is still available we strongly encourage the 31 | ## use of select(). 32 | ls("package:@ANNOBJPREFIX@.db") 33 | } 34 | 35 | \keyword{datasets} 36 | 37 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/YEASTCHIP.DB/man/BASE.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@.db} 2 | \alias{@ANNOBJPREFIX@.db} 3 | \alias{@ANNOBJPREFIX@} 4 | \title{Bioconductor annotation data package} 5 | \description{ 6 | 7 | Welcome to the @ANNOBJPREFIX@.db annotation Package. The purpose of 8 | this package is to provide detailed information about the 9 | @ANNOBJPREFIX@ platform. This package is updated biannually. 10 | 11 | Objects in this package are accessed using the \code{select()} interface. 12 | See ?select in the AnnotationDbi package for details. 13 | } 14 | 15 | \seealso{ 16 | \itemize{ 17 | \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of 18 | \code{keys()}, \code{columns()} and \code{select()}. 19 | } 20 | } 21 | 22 | \examples{ 23 | ## select() interface: 24 | ## Objects in this package can be accessed using the select() interface 25 | ## from the AnnotationDbi package. See ?select for details. 26 | columns(@ANNOBJPREFIX@.db) 27 | 28 | ## Bimap interface: 29 | ## The 'old style' of interacting with these objects is manipulation as 30 | ## bimaps. While this approach is still available we strongly encourage the 31 | ## use of select(). 32 | ls("package:@ANNOBJPREFIX@.db") 33 | } 34 | 35 | \keyword{datasets} 36 | 37 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/YEASTNCBI.DB/man/BASE.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@.db} 2 | \alias{@ANNOBJPREFIX@.db} 3 | \alias{@ANNOBJPREFIX@} 4 | \title{Bioconductor annotation data package} 5 | \description{ 6 | 7 | Welcome to the @ANNOBJPREFIX@.db annotation Package. The purpose of 8 | this package is to provide detailed information about the 9 | @ANNOBJPREFIX@ platform. This package is updated biannually. 10 | 11 | Objects in this package are accessed using the \code{select()} interface. 12 | See ?select in the AnnotationDbi package for details. 13 | } 14 | 15 | \seealso{ 16 | \itemize{ 17 | \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of 18 | \code{keys()}, \code{columns()} and \code{select()}. 19 | } 20 | } 21 | 22 | \examples{ 23 | ## select() interface: 24 | ## Objects in this package can be accessed using the select() interface 25 | ## from the AnnotationDbi package. See ?select for details. 26 | columns(@ANNOBJPREFIX@.db) 27 | 28 | ## Bimap interface: 29 | ## The 'old style' of interacting with these objects is manipulation as 30 | ## bimaps. While this approach is still available we strongly encourage the 31 | ## use of select(). 32 | ls("package:@ANNOBJPREFIX@.db") 33 | } 34 | 35 | \keyword{datasets} 36 | 37 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/ARABIDOPSISCHIP.DB/man/BASE.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@.db} 2 | \alias{@ANNOBJPREFIX@.db} 3 | \alias{@ANNOBJPREFIX@} 4 | \title{Bioconductor annotation data package} 5 | \description{ 6 | 7 | Welcome to the @ANNOBJPREFIX@.db annotation Package. The purpose of 8 | this package is to provide detailed information about the 9 | @ANNOBJPREFIX@ platform. This package is updated biannually. 10 | 11 | Objects in this package are accessed using the \code{select()} interface. 12 | See ?select in the AnnotationDbi package for details. 13 | } 14 | 15 | \seealso{ 16 | \itemize{ 17 | \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of 18 | \code{keys()}, \code{columns()} and \code{select()}. 19 | } 20 | } 21 | 22 | \examples{ 23 | ## select() interface: 24 | ## Objects in this package can be accessed using the select() interface 25 | ## from the AnnotationDbi package. See ?select for details. 26 | columns(@ANNOBJPREFIX@.db) 27 | 28 | ## Bimap interface: 29 | ## The 'old style' of interacting with these objects is manipulation as 30 | ## bimaps. While this approach is still available we strongly encourage the 31 | ## use of select(). 32 | ls("package:@ANNOBJPREFIX@.db") 33 | } 34 | 35 | \keyword{datasets} 36 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/COELICOLOR.DB/man/PROTEINGI.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@PROTEINGI} 2 | \alias{@ANNOBJPREFIX@PROTEINGI} 3 | \title{Map Entrez Gene IDs to protein GenInfo (GI) numbers} 4 | \description{ 5 | @ANNOBJPREFIX@PROTEINGI is an R object that provides mappings between entrez gene 6 | identifiers and the protein GI number associated to the gene of interest. 7 | } 8 | \details{ 9 | Each entrez gene identifier maps to a protein gi number. 10 | 11 | Mappings were based on data provided by: @PROTEINGISOURCE@ 12 | } 13 | 14 | \seealso{ 15 | \itemize{ 16 | \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of 17 | the \code{select()} interface. 18 | } 19 | } 20 | 21 | \examples{ 22 | ## select() interface: 23 | ## Objects in this package can be accessed using the select() interface 24 | ## from the AnnotationDbi package. See ?select for details. 25 | 26 | ## Bimap interface: 27 | x <- @ANNOBJPREFIX@PROTEINGI 28 | # Get the entrez gene identifiers that are mapped to a protein GI number 29 | mapped_genes <- mappedkeys(x) 30 | # Convert to a list 31 | xx <- as.list(x[mapped_genes]) 32 | if(length(xx) > 0) { 33 | # Get the PROTEINGI for the first five genes 34 | xx[1:5] 35 | # Get the first one 36 | xx[[1]] 37 | } 38 | } 39 | 40 | \keyword{datasets} 41 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/COELICOLOR.DB/man/LOCUSTAG.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@LOCUSTAG} 2 | \alias{@ANNOBJPREFIX@LOCUSTAG} 3 | \title{Map Entrez Gene IDs to Locus Tag IDs} 4 | \description{ 5 | @ANNOBJPREFIX@LOCUSTAG is an R object that provides mappings between entrez gene 6 | identifiers and the locus tag identifier associated to the gene of interest. 7 | } 8 | \details{ 9 | Each entrez gene identifier maps to a locus tag identifier. 10 | 11 | Mappings were based on data provided by: @LOCUSTAGSOURCE@ 12 | } 13 | 14 | \seealso{ 15 | \itemize{ 16 | \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of 17 | the \code{select()} interface. 18 | } 19 | } 20 | 21 | \examples{ 22 | ## select() interface: 23 | ## Objects in this package can be accessed using the select() interface 24 | ## from the AnnotationDbi package. See ?select for details. 25 | 26 | ## Bimap interface: 27 | x <- @ANNOBJPREFIX@LOCUSTAG 28 | # Get the entrez gene identifiers that are mapped to a locus tag 29 | mapped_genes <- mappedkeys(x) 30 | # Convert to a list 31 | xx <- as.list(x[mapped_genes]) 32 | if(length(xx) > 0) { 33 | # Get the LOCUSTAG for the first five genes 34 | xx[1:5] 35 | # Get the first one 36 | xx[[1]] 37 | } 38 | } 39 | \keyword{datasets} 40 | 41 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/GO.DB/man/OBSOLETE.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@OBSOLETE} 2 | \alias{@ANNOBJPREFIX@OBSOLETE} 3 | \title{Annotation of GO identifiers by terms defined by Gene Ontology 4 | Consortium and their status are obsolete} 5 | \description{ 6 | This is an R object mapping GO identifiers to the specific 7 | terms in defined by Gene Ontology Consortium and their definition are obsolete 8 | } 9 | \details{ 10 | All the obsolete GO terms that are collected in this index will no longer exist 11 | in other mapping objects. 12 | 13 | Mappings were based on data provided by: @OBSOLETESOURCE@ 14 | 15 | } 16 | \references{ 17 | \url{https://www.ncib.nlm.nih.gov/LocusLink} 18 | } 19 | 20 | \seealso{ 21 | \itemize{ 22 | \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of 23 | the \code{select()} interface. 24 | } 25 | } 26 | 27 | \examples{ 28 | ## select() interface: 29 | ## Objects in this package can be accessed using the select() interface 30 | ## from the AnnotationDbi package. See ?select for details. 31 | 32 | ## Bimap interface: 33 | # Convert the object to a list 34 | xx <- as.list(@ANNOBJPREFIX@TERM) 35 | if(length(xx) > 0){ 36 | # Get the TERMS for the first elent of xx 37 | GOID(xx[[1]]) 38 | Ontology(xx[[1]]) 39 | } 40 | } 41 | \keyword{datasets} 42 | 43 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/NCBICHIP.DB/man/ZFIN.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@ZFIN} 2 | \alias{@ANNOBJPREFIX@ZFIN} 3 | \alias{@ANNOBJPREFIX@ZFIN2PROBE} 4 | \title{Map Zfin accession numbers with Entrez Gene identifiers} 5 | \description{ 6 | @ANNOBJPREFIX@ZFIN is an R object that contains mappings between 7 | Entrez Gene identifiers and Zfin accession numbers. 8 | } 9 | 10 | \details{ 11 | This object is a simple mapping of manufacturer identifiers to Zfin 12 | Accessions. 13 | 14 | Mappings were based on data provided by: @ZFINSOURCE@ 15 | } 16 | 17 | \seealso{ 18 | \itemize{ 19 | \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of 20 | the \code{select()} interface. 21 | } 22 | } 23 | 24 | \examples{ 25 | ## select() interface: 26 | ## Objects in this package can be accessed using the select() interface 27 | ## from the AnnotationDbi package. See ?select for details. 28 | 29 | ## Bimap interface: 30 | x <- @ANNOBJPREFIX@ZFIN 31 | # Get the entrez gene IDs that are mapped to an Zfin ID 32 | mapped_genes <- mappedkeys(x) 33 | # Convert to a list 34 | xx <- as.list(x[mapped_genes][1:300]) 35 | if(length(xx) > 0) { 36 | # Get the Zfin IDs for the first five genes 37 | xx[1:5] 38 | # Get the first one 39 | xx[[1]] 40 | } 41 | } 42 | 43 | \keyword{datasets} 44 | 45 | 46 | 47 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/NCBIORG.DB/man/BASE.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@.db} 2 | \alias{@ANNOBJPREFIX@.db} 3 | \alias{@ANNOBJPREFIX@} 4 | \title{Bioconductor annotation data package} 5 | \description{ 6 | 7 | Welcome to the @ANNOBJPREFIX@.db annotation Package. This is an 8 | organism specific package. The purpose is to provide detailed 9 | information about the species abbreviated in the second part of the 10 | package name @ANNOBJPREFIX@.db. This package is updated biannually. 11 | 12 | Objects in this package are accessed using the \code{select()} interface. 13 | See ?select in the AnnotationDbi package for details. 14 | } 15 | 16 | \seealso{ 17 | \itemize{ 18 | \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of 19 | \code{keys()}, \code{columns()} and \code{select()}. 20 | } 21 | } 22 | 23 | \examples{ 24 | ## select() interface: 25 | ## Objects in this package can be accessed using the select() interface 26 | ## from the AnnotationDbi package. See ?select for details. 27 | columns(@ANNOBJPREFIX@.db) 28 | 29 | ## Bimap interface: 30 | ## The 'old style' of interacting with these objects is manipulation as 31 | ## bimaps. While this approach is still available we strongly encourage the 32 | ## use of select(). 33 | ls("package:@ANNOBJPREFIX@.db") 34 | } 35 | \keyword{datasets} 36 | 37 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/COELICOLOR.DB/man/BASE.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@.db} 2 | \alias{@ANNOBJPREFIX@.db} 3 | \alias{@ANNOBJPREFIX@} 4 | \title{Bioconductor annotation data package} 5 | \description{ 6 | 7 | Welcome to the @ANNOBJPREFIX@.db annotation Package. This is an 8 | organism specific package. The purpose is to provide detailed 9 | information about the species abbreviated in the second part of the 10 | package name @ANNOBJPREFIX@.db. This package is updated biannually. 11 | 12 | Objects in this package are accessed using the \code{select()} interface. 13 | See ?select in the AnnotationDbi package for details. 14 | } 15 | 16 | \seealso{ 17 | \itemize{ 18 | \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of 19 | \code{keys()}, \code{columns()} and \code{select()}. 20 | } 21 | } 22 | 23 | \examples{ 24 | ## select() interface: 25 | ## Objects in this package can be accessed using the select() interface 26 | ## from the AnnotationDbi package. See ?select for details. 27 | columns(@ANNOBJPREFIX@.db) 28 | 29 | ## Bimap interface: 30 | ## The 'old style' of interacting with these objects is manipulation as 31 | ## bimaps. While this approach is still available we strongly encourage the 32 | ## use of select(). 33 | ls("package:@ANNOBJPREFIX@.db") 34 | } 35 | 36 | \keyword{datasets} 37 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/MALARIA.DB/man/BASE.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@.db} 2 | \alias{@ANNOBJPREFIX@.db} 3 | \alias{@ANNOBJPREFIX@} 4 | \title{Bioconductor annotation data package} 5 | \description{ 6 | 7 | Welcome to the @ANNOBJPREFIX@.db annotation Package. This is an 8 | organism specific package. The purpose is to provide detailed 9 | information about the species abbreviated in the second part of the 10 | package name @ANNOBJPREFIX@.db. This package is updated biannually. 11 | 12 | Objects in this package are accessed using the \code{select()} interface. 13 | See ?select in the AnnotationDbi package for details. 14 | } 15 | 16 | \seealso{ 17 | \itemize{ 18 | \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of 19 | \code{keys()}, \code{columns()} and \code{select()}. 20 | } 21 | } 22 | 23 | \examples{ 24 | ## select() interface: 25 | ## Objects in this package can be accessed using the select() interface 26 | ## from the AnnotationDbi package. See ?select for details. 27 | columns(@ANNOBJPREFIX@.db) 28 | 29 | ## Bimap interface: 30 | ## The 'old style' of interacting with these objects is manipulation as 31 | ## bimaps. While this approach is still available we strongly encourage the 32 | ## use of select(). 33 | ls("package:@ANNOBJPREFIX@.db") 34 | } 35 | 36 | \keyword{datasets} 37 | 38 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/YEAST.DB/man/BASE.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@.db} 2 | \alias{@ANNOBJPREFIX@.db} 3 | \alias{@ANNOBJPREFIX@} 4 | \title{Bioconductor annotation data package} 5 | \description{ 6 | 7 | Welcome to the @ANNOBJPREFIX@.db annotation Package. This is an 8 | organism specific package. The purpose is to provide detailed 9 | information about the species abbreviated in the second part of the 10 | package name @ANNOBJPREFIX@.db. This package is updated biannually. 11 | 12 | Objects in this package are accessed using the \code{select()} interface. 13 | See ?select in the AnnotationDbi package for details. 14 | } 15 | 16 | \seealso{ 17 | \itemize{ 18 | \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of 19 | \code{keys()}, \code{columns()} and \code{select()}. 20 | } 21 | } 22 | 23 | \examples{ 24 | ## select() interface: 25 | ## Objects in this package can be accessed using the select() interface 26 | ## from the AnnotationDbi package. See ?select for details. 27 | columns(@ANNOBJPREFIX@.db) 28 | 29 | ## Bimap interface: 30 | ## The 'old style' of interacting with these objects is manipulation as 31 | ## bimaps. While this approach is still available we strongly encourage the 32 | ## use of select(). 33 | ls("package:@ANNOBJPREFIX@.db") 34 | } 35 | 36 | \keyword{datasets} 37 | 38 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/ORGANISM.DB/man/BASE.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@.db} 2 | \alias{@ANNOBJPREFIX@.db} 3 | \alias{@ANNOBJPREFIX@} 4 | \title{Bioconductor annotation data package} 5 | \description{ 6 | 7 | Welcome to the @ANNOBJPREFIX@.db annotation Package. This is an 8 | organism specific package. The purpose is to provide detailed 9 | information about the species abbreviated in the second part of the 10 | package name @ANNOBJPREFIX@.db. This package is updated biannually. 11 | 12 | Objects in this package are accessed using the \code{select()} interface. 13 | See ?select in the AnnotationDbi package for details. 14 | } 15 | 16 | \seealso{ 17 | \itemize{ 18 | \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of 19 | \code{keys()}, \code{columns()} and \code{select()}. 20 | } 21 | } 22 | 23 | \examples{ 24 | ## select() interface: 25 | ## Objects in this package can be accessed using the select() interface 26 | ## from the AnnotationDbi package. See ?select for details. 27 | columns(@ANNOBJPREFIX@.db) 28 | 29 | ## Bimap interface: 30 | ## The 'old style' of interacting with these objects is manipulation as 31 | ## bimaps. While this approach is still available we strongly encourage the 32 | ## use of select(). 33 | ls("package:@ANNOBJPREFIX@.db") 34 | } 35 | 36 | \keyword{datasets} 37 | 38 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/NCBICHIP.DB/man/WORMBASE.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@WORMBASE} 2 | \alias{@ANNOBJPREFIX@WORMBASE} 3 | \alias{@ANNOBJPREFIX@WORMBASE2PROBE} 4 | \title{Map Wormbase accession numbers with Entrez Gene identifiers} 5 | \description{ 6 | @ANNOBJPREFIX@WORMBASE is an R object that contains mappings between 7 | manufacturer identifiers and Wormbase accession numbers. 8 | } 9 | \details{ 10 | This object is a simple mapping of manufacturer identifiers to Wormbase 11 | Accessions. 12 | 13 | Mappings were based on data provided from ensembl 14 | } 15 | 16 | \seealso{ 17 | \itemize{ 18 | \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of 19 | the \code{select()} interface. 20 | } 21 | } 22 | 23 | \examples{ 24 | ## select() interface: 25 | ## Objects in this package can be accessed using the select() interface 26 | ## from the AnnotationDbi package. See ?select for details. 27 | 28 | ## Bimap interface: 29 | x <- @ANNOBJPREFIX@WORMBASE 30 | # Get the entrez gene IDs that are mapped to an Wormbase ID 31 | mapped_genes <- mappedkeys(x) 32 | # Convert to a list 33 | xx <- as.list(x[mapped_genes][1:300]) 34 | if(length(xx) > 0) { 35 | # Get the Wormbase IDs for the first five genes 36 | xx[1:5] 37 | # Get the first one 38 | xx[[1]] 39 | } 40 | } 41 | \keyword{datasets} 42 | 43 | 44 | 45 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/NCBIORG.DB/man/ZFIN.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@ZFIN} 2 | \alias{@ANNOBJPREFIX@ZFIN} 3 | \title{Map Zfin accession numbers with Entrez Gene identifiers} 4 | \description{ 5 | @ANNOBJPREFIX@ZFIN is an R object that contains mappings between 6 | Entrez Gene identifiers and Zfin accession numbers. 7 | } 8 | 9 | \details{ 10 | This object is a simple mapping of Entrez Gene identifiers 11 | \url{https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene} to Zfin 12 | Accession Numbers. 13 | 14 | Mappings were based on data provided by: @ZFINSOURCE@ 15 | } 16 | 17 | \seealso{ 18 | \itemize{ 19 | \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of 20 | the \code{select()} interface. 21 | } 22 | } 23 | 24 | \examples{ 25 | ## select() interface: 26 | ## Objects in this package can be accessed using the select() interface 27 | ## from the AnnotationDbi package. See ?select for details. 28 | 29 | ## Bimap interface: 30 | x <- @ANNOBJPREFIX@ZFIN 31 | # Get the entrez gene IDs that are mapped to a Zfin ID 32 | mapped_genes <- mappedkeys(x) 33 | # Convert to a list 34 | xx <- as.list(x[mapped_genes]) 35 | if(length(xx) > 0) { 36 | # Get the Zfin gene IDs for the first five genes 37 | xx[1:5] 38 | # Get the first one 39 | xx[[1]] 40 | } 41 | } 42 | 43 | \keyword{datasets} 44 | 45 | 46 | 47 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/YEASTNCBI.DB/man/UNIPROT.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@UNIPROT} 2 | \alias{@ANNOBJPREFIX@UNIPROT} 3 | \title{Map Uniprot accession numbers with Entrez Gene identifiers} 4 | \description{ 5 | @ANNOBJPREFIX@UNIPROT is an R object that contains mappings between 6 | Entrez Gene identifiers and Uniprot accession numbers. 7 | } 8 | 9 | \details{ 10 | This object is a simple mapping of Entrez Gene identifiers 11 | \url{https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene} to Uniprot 12 | Accession Numbers. 13 | 14 | Mappings were based on data provided by: @UNIPROTSOURCE@ 15 | } 16 | 17 | \seealso{ 18 | \itemize{ 19 | \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of 20 | the \code{select()} interface. 21 | } 22 | } 23 | 24 | \examples{ 25 | ## select() interface: 26 | ## Objects in this package can be accessed using the select() interface 27 | ## from the AnnotationDbi package. See ?select for details. 28 | 29 | ## Bimap interface: 30 | x <- @ANNOBJPREFIX@UNIPROT 31 | # Get the entrez gene IDs that are mapped to a Uniprot ID 32 | mapped_genes <- mappedkeys(x) 33 | # Convert to a list 34 | xx <- as.list(x[mapped_genes]) 35 | if(length(xx) > 0) { 36 | # Get the Uniprot gene IDs for the first five genes 37 | xx[1:5] 38 | # Get the first one 39 | xx[[1]] 40 | } 41 | } 42 | 43 | \keyword{datasets} 44 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/KEGG.DB/man/PATHID2NAME.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@PATHID2NAME} 2 | \alias{@ANNOBJPREFIX@PATHID2NAME} 3 | \title{An annotation data object that maps KEGG pathway identifiers to 4 | KEGG pathway names} 5 | \description{ 6 | @ANNOBJPREFIX@PATHID2NAME maps KEGG pathway identifiers to pathway names used by 7 | KEGG for various pathways 8 | } 9 | \details{ 10 | This is an R object containing key and value pairs. Keys are 11 | KEGG pathway identifiers and values are pathway names. Values are vectors of 12 | length 1. 13 | 14 | Mappings were based on data provided by: @PATHID2NAMESOURCE@ 15 | 16 | } 17 | 18 | \references{ 19 | \url{ftp://ftp.genome.ad.jp/pub/kegg/pathways} 20 | } 21 | 22 | \seealso{ 23 | \itemize{ 24 | \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of 25 | the \code{select()} interface. 26 | } 27 | } 28 | 29 | \examples{ 30 | ## select() interface: 31 | ## Objects in this package can be accessed using the select() interface 32 | ## from the AnnotationDbi package. See ?select for details. 33 | 34 | ## Bimap interface: 35 | xx <- as.list(@ANNOBJPREFIX@PATHID2NAME) 36 | if(length(xx) > 0){ 37 | # get the value for the first key 38 | xx[[1]] 39 | # Get the values for a few keys 40 | if(length(xx) >= 3){ 41 | xx[1:3] 42 | } 43 | } 44 | } 45 | \keyword{datasets} 46 | 47 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/YEAST.DB/man/COMMON2ORF.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@COMMON2ORF} 2 | \alias{@ANNOBJPREFIX@COMMON2ORF} 3 | \title{Map Between Yeast Common Names and ORF Identifiers} 4 | \description{ 5 | @ANNOBJPREFIX@COMMON2ORF is an R object that maps 6 | the yeast common names (gene names and aliases) to the 7 | corresponding yeast ORF identifiers. 8 | } 9 | \details{ 10 | Each yeast common name, either gene name or alias, maps to 11 | a vector of ORF identifiers. This mapping is the reverse 12 | mappings of @ANNOBJPREFIX@GENENAME. 13 | 14 | Mappings were based on data provided by: 15 | 16 | @COMMON2ORFSOURCE@ 17 | } 18 | 19 | \seealso{ 20 | \itemize{ 21 | \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of 22 | the \code{select()} interface. 23 | } 24 | } 25 | 26 | \examples{ 27 | ## select() interface: 28 | ## Objects in this package can be accessed using the select() interface 29 | ## from the AnnotationDbi package. See ?select for details. 30 | 31 | ## Bimap interface: 32 | # Convert to a list 33 | xx <- as.list(@ANNOBJPREFIX@COMMON2ORF) 34 | # Remove probes that do not map in COMMON2ORF 35 | xx <- xx[!is.na(xx)] 36 | if(length(xx) > 0){ 37 | # Gets the ORF identifiers for the first five gene names/alias 38 | xx[1:5] 39 | # Get the first one 40 | xx[[1]] 41 | } 42 | } 43 | \keyword{datasets} 44 | 45 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/ARABIDOPSISCHIP.DB/man/ORGANISM.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@ORGANISM} 2 | \alias{@ANNOBJPREFIX@ORGANISM} 3 | \alias{@ANNOBJPREFIX@ORGPKG} 4 | 5 | \title{The Organism information for @ANNOBJPREFIX@} 6 | \description{ 7 | @ANNOBJPREFIX@ORGANISM is an R object that contains a single item: a 8 | character string that names the organism for which @ANNOBJPREFIX@ was 9 | built. 10 | @ANNOBJPREFIX@ORGPKG is an R object that contains a chararcter vector 11 | with the name of the organism package that a chip package depends on 12 | for its gene-centric annotation. 13 | } 14 | \details{ 15 | Although the package name is suggestive of the organism for which it 16 | was built, @ANNOBJPREFIX@ORGANISM provides a simple way to programmatically 17 | extract the organism name. 18 | @ANNOBJPREFIX@ORGPKG provides a simple way to programmatically 19 | extract the name of the parent organism package. The parent organism 20 | package is a strict dependency for chip packages as this is where the 21 | gene cetric information is ultimately extracted from. The full 22 | package name will always be this string plus the extension ".db". But 23 | most programatic access will not require this extension, so its more 24 | convenient to leave it out. 25 | } 26 | \examples{ 27 | @ANNOBJPREFIX@ORGANISM 28 | @ANNOBJPREFIX@ORGPKG 29 | } 30 | \keyword{datasets} 31 | 32 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/NCBIORG.DB/man/WORMBASE.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@WORMBASE} 2 | \alias{@ANNOBJPREFIX@WORMBASE} 3 | \title{Map Wormbase accession numbers with Entrez Gene identifiers} 4 | \description{ 5 | @ANNOBJPREFIX@WORMBASE is an R object that contains mappings between 6 | Entrez Gene identifiers and Wormbase accession numbers. 7 | } 8 | 9 | \details{ 10 | This object is a simple mapping of Entrez Gene identifiers 11 | \url{https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene} to Wormbase 12 | Accession Numbers. 13 | 14 | Mappings were based on data provided from ensembl 15 | } 16 | 17 | \seealso{ 18 | \itemize{ 19 | \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of 20 | the \code{select()} interface. 21 | } 22 | } 23 | 24 | \examples{ 25 | ## select() interface: 26 | ## Objects in this package can be accessed using the select() interface 27 | ## from the AnnotationDbi package. See ?select for details. 28 | 29 | ## Bimap interface: 30 | x <- @ANNOBJPREFIX@WORMBASE 31 | # Get the entrez gene IDs that are mapped to a Wormbase ID 32 | mapped_genes <- mappedkeys(x) 33 | # Convert to a list 34 | xx <- as.list(x[mapped_genes]) 35 | if(length(xx) > 0) { 36 | # Get the Wormbase gene IDs for the first five genes 37 | xx[1:5] 38 | # Get the first one 39 | xx[[1]] 40 | } 41 | } 42 | 43 | \keyword{datasets} 44 | 45 | 46 | 47 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/YEAST.DB/man/UNIPROT.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@UNIPROT} 2 | \alias{@ANNOBJPREFIX@UNIPROT} 3 | \title{Map Uniprot accession numbers with Systematic ORF identifiers} 4 | \description{ 5 | @ANNOBJPREFIX@UNIPROT is an R object that contains mappings between 6 | Systematic ORF identifiers and Uniprot accession numbers. 7 | } 8 | \details{ 9 | This object is a simple mapping of Systematic ORF identifiers 10 | \url{https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene} to Uniprot 11 | Accession Numbers. 12 | 13 | Mappings were based on data provided by: @UNIPROTSOURCE@ 14 | } 15 | 16 | \seealso{ 17 | \itemize{ 18 | \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of 19 | the \code{select()} interface. 20 | } 21 | } 22 | 23 | \examples{ 24 | ## select() interface: 25 | ## Objects in this package can be accessed using the select() interface 26 | ## from the AnnotationDbi package. See ?select for details. 27 | 28 | ## Bimap interface: 29 | x <- @ANNOBJPREFIX@UNIPROT 30 | # Get the Systematic ORF IDs that are mapped to a Uniprot ID 31 | mapped_genes <- mappedkeys(x) 32 | # Convert to a list 33 | xx <- as.list(x[mapped_genes]) 34 | if(length(xx) > 0) { 35 | # Get the Uniprot gene IDs for the first five genes 36 | xx[1:5] 37 | # Get the first one 38 | xx[[1]] 39 | } 40 | } 41 | 42 | \keyword{datasets} 43 | 44 | 45 | 46 | -------------------------------------------------------------------------------- /NAMESPACE: -------------------------------------------------------------------------------- 1 | import(methods) 2 | importFrom(utils, available.packages, download.file, installed.packages, 3 | packageDescription, read.csv, read.delim, read.table, 4 | str, untar, unzip, write.table) 5 | import(Biobase) 6 | import(DBI) 7 | import(RSQLite) 8 | import(BiocGenerics) 9 | import(S4Vectors) 10 | import(AnnotationDbi) 11 | import(XML) 12 | importFrom(RCurl, getURL) 13 | 14 | exportClasses( 15 | ## from R/AnnDbPkg-maker.R 16 | "AnnDbPkgSeed" 17 | 18 | ) 19 | 20 | exportMethods( 21 | "makeAnnDbPkg" 22 | ) 23 | 24 | export( 25 | ## from R/AnnDbPkg-maker.R 26 | loadAnnDbPkgIndex, makeAnnDbPkg, 27 | 28 | ## help functions for making sqlite files 29 | populateDB, 30 | 31 | ## wrapper functions for making chip packages 32 | makeDBPackage, 33 | 34 | available.db0pkgs, 35 | available.dbschemas, 36 | available.chipdbschemas, 37 | 38 | #Convenience function to make the intermediate DB pkgs 39 | wrapBaseDBPackages, 40 | 41 | ## This one will make you an org package: 42 | makeOrgPackageFromNCBI, 43 | 44 | ## This one will make you an org package from just data.frames: 45 | makeOrgPackage, 46 | makeChipPackage, 47 | 48 | ## from R/makeProbePackage.R 49 | getProbeDataAffy, 50 | getProbeData_1lq, 51 | makeProbePackage, 52 | makeInpDb 53 | ) 54 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/YEAST.DB/man/ENTREZID.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@ENTREZID} 2 | \alias{@ANNOBJPREFIX@ENTREZID} 3 | \title{Map Systematic ORF identifiers with Entrez Gene identifiers} 4 | \description{ 5 | @ANNOBJPREFIX@ENTREZID is an R object that contains mappings between 6 | Systematic ORF accession numbers and NCBI Entrez Gene identifiers. 7 | } 8 | \details{ 9 | This object is a simple mapping of Entrez Gene identifiers 10 | \url{https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene} to 11 | systematic ORF locus Accession Numbers. 12 | 13 | Mappings were based on data provided by: @ENTREZIDSOURCE@ 14 | } 15 | 16 | \seealso{ 17 | \itemize{ 18 | \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of 19 | the \code{select()} interface. 20 | } 21 | } 22 | 23 | \examples{ 24 | ## select() interface: 25 | ## Objects in this package can be accessed using the select() interface 26 | ## from the AnnotationDbi package. See ?select for details. 27 | 28 | ## Bimap interface: 29 | x <- @ANNOBJPREFIX@ENTREZID 30 | # Get the ORF IDs that are mapped to an Entrez Gene ID 31 | mapped_genes <- mappedkeys(x) 32 | # Convert to a list 33 | xx <- as.list(x[mapped_genes]) 34 | if(length(xx) > 0) { 35 | # Get the Entrez gene IDs for the first five genes 36 | xx[1:5] 37 | # Get the first one 38 | xx[[1]] 39 | } 40 | } 41 | \keyword{datasets} 42 | 43 | 44 | 45 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/ARABIDOPSIS.DB/man/ENTREZID.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@ENTREZID} 2 | \alias{@ANNOBJPREFIX@ENTREZID} 3 | \title{Map TAIR identifiers with Entrez Gene identifiers} 4 | \description{ 5 | @ANNOBJPREFIX@ENTREZID is an R object that contains mappings between 6 | TAIR accession numbers and NCBI Entrez Gene identifiers. 7 | } 8 | \details{ 9 | This object is a simple mapping of Entrez Gene identifiers 10 | \url{https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene} to 11 | TAIR Accession Numbers. 12 | 13 | Mappings were based on data provided by: 14 | \url{ftp://ftp.ncbi.nlm.nih.gov/gene/DATA} 15 | } 16 | 17 | \seealso{ 18 | \itemize{ 19 | \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of 20 | the \code{select()} interface. 21 | } 22 | } 23 | 24 | \examples{ 25 | ## select() interface: 26 | ## Objects in this package can be accessed using the select() interface 27 | ## from the AnnotationDbi package. See ?select for details. 28 | 29 | ## Bimap interface: 30 | x <- @ANNOBJPREFIX@ENTREZID 31 | # Get the ORF IDs that are mapped to an Entrez Gene ID 32 | mapped_genes <- mappedkeys(x) 33 | # Convert to a list 34 | xx <- as.list(x[mapped_genes]) 35 | if(length(xx) > 0) { 36 | # Get the Entrez gene IDs for the first five genes 37 | xx[1:5] 38 | # Get the first one 39 | xx[[1]] 40 | } 41 | } 42 | \keyword{datasets} 43 | 44 | 45 | 46 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/KEGG.DB/man/PATHNAME2ID.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@PATHNAME2ID} 2 | \alias{@ANNOBJPREFIX@PATHNAME2ID} 3 | \title{An annotation data object that maps KEGG pathway names to 4 | identifiers for the corresponding pathway names used by KEGG} 5 | \description{ 6 | @ANNOBJPREFIX@PATHNAME2ID maps KEGG pathway names to pathway identifiers used by 7 | KEGG for various pathways 8 | } 9 | \details{ 10 | This is an R object containing key and value pairs. Keys are 11 | KEGG pathway names and values are pathway identifiers. Values are vectors of 12 | length 1. 13 | 14 | Mappings were based on data provided by: @PATHNAME2IDSOURCE@ 15 | } 16 | 17 | \references{ 18 | \url{ftp://ftp.genome.ad.jp/pub/kegg/pathways} 19 | } 20 | 21 | \seealso{ 22 | \itemize{ 23 | \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of 24 | the \code{select()} interface. 25 | } 26 | } 27 | 28 | \examples{ 29 | ## select() interface: 30 | ## Objects in this package can be accessed using the select() interface 31 | ## from the AnnotationDbi package. See ?select for details. 32 | 33 | ## Bimap interface: 34 | xx <- as.list(@ANNOBJPREFIX@PATHNAME2ID) 35 | if(length(xx) > 0){ 36 | # get the value for the first key 37 | xx[[1]] 38 | # Get the values for a few keys 39 | if(length(xx) >= 3){ 40 | xx[1:3] 41 | } 42 | } 43 | } 44 | \keyword{datasets} 45 | 46 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/ORGANISM.DB/man/ACCNUM.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@ACCNUM} 2 | \alias{@ANNOBJPREFIX@ACCNUM} 3 | \alias{@ANNOBJPREFIX@ACCNUM2EG} 4 | \title{Map Entrez Gene identifiers to GenBank Accession Numbers} 5 | \description{ 6 | @ANNOBJPREFIX@ACCNUM is an R object that contains mappings between 7 | Entrez Gene identifiers and GenBank accession numbers. 8 | } 9 | \details{ 10 | This object is a simple mapping of Entrez Gene identifiers 11 | \url{https://www.ncib.nlm.nih.gov/entrez/query.fcgi?db=gene} to all possible GenBank 12 | accession numbers. 13 | 14 | Mappings were based on data provided by: @ACCNUMSOURCE@ 15 | } 16 | 17 | \seealso{ 18 | \itemize{ 19 | \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of 20 | the \code{select()} interface. 21 | } 22 | } 23 | 24 | \examples{ 25 | ## select() interface: 26 | ## Objects in this package can be accessed using the select() interface 27 | ## from the AnnotationDbi package. See ?select for details. 28 | 29 | ## Bimap interface: 30 | x <- @ANNOBJPREFIX@ACCNUM 31 | # Get the entrez gene identifiers that are mapped to an ACCNUM 32 | mapped_genes <- mappedkeys(x) 33 | # Convert to a list 34 | xx <- as.list(x[mapped_genes]) 35 | if(length(xx) > 0) { 36 | # Get the ACCNUM for the first five genes 37 | xx[1:5] 38 | # Get the first one 39 | xx[[1]] 40 | } 41 | } 42 | 43 | \keyword{datasets} 44 | 45 | 46 | 47 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/KEGG.DB/man/GO2ENZYMEID.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@GO2ENZYMEID} 2 | \alias{@ANNOBJPREFIX@GO2ENZYMEID} 3 | \title{An annotation data object that maps Gene Ontology (GO) identifiers to 4 | Enzyme Commission numbers} 5 | \description{ 6 | @ANNOBJPREFIX@GO2ENZYMEID maps GO identifiers to Enzyme Commission numbers 7 | } 8 | 9 | \details{ 10 | This is an R object containing key and value pairs. Keys are 11 | GO identifiers and values are Enzyme Commission numbers. Values are vectors of 12 | length 1. GO identifiers can not be mapped to any Enzyme Commission number are 13 | assigned NAs. 14 | 15 | Mappings are based on data provided by: @GO2ENZYMEIDSOURCE@ 16 | } 17 | 18 | \references{ 19 | \url{ftp://ftp.genome.ad.jp/pub/kegg/pathways} 20 | } 21 | 22 | \seealso{ 23 | \itemize{ 24 | \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of 25 | the \code{select()} interface. 26 | } 27 | } 28 | 29 | \examples{ 30 | ## select() interface: 31 | ## Objects in this package can be accessed using the select() interface 32 | ## from the AnnotationDbi package. See ?select for details. 33 | 34 | ## Bimap interface: 35 | xx <- as.list(@ANNOBJPREFIX@GO2ENZYMEID) 36 | if(length(xx) > 0){ 37 | # Get the value of the first key 38 | xx[[1]] 39 | # Get values for a few keys 40 | if(length(xx) >= 3){ 41 | xx[1:3] 42 | } 43 | } 44 | } 45 | \keyword{datasets} 46 | 47 | -------------------------------------------------------------------------------- /man/makeInpDb.Rd: -------------------------------------------------------------------------------- 1 | \name{makeInpDb} 2 | 3 | \alias{makeInpDb} 4 | 5 | \title{ 6 | Builds an individual DB from online files at inparanoid that is in 7 | turn meant for generating Inparanoid 8 based objects. 8 | } 9 | \description{ 10 | This is really meant to be used by AnnotationHubData for eventual 11 | exposure through the AnnotationHub. Users who are interested in 12 | Inparanoid 8 should look for the relevant objects to be in 13 | AnnotationHub. This function is just a database builder that allows 14 | us to put the data up there. So this is not really intended for use 15 | by end users. 16 | } 17 | \usage{ 18 | makeInpDb(dir, dataDir) 19 | } 20 | \arguments{ 21 | \item{dir}{the full path to the online Inparanpoid 8 resource.} 22 | \item{dataDir}{directory where the source inparanoid.sqlite DB is} 23 | } 24 | \value{ A SQLite DB is produced but this is not returned from the 25 | function. loadDb is expected to be used by AnnotationHub to convert 26 | these into objects after the sqlite DB is downloaded from the hub server. } 27 | \author{ 28 | M. Carlson 29 | } 30 | \examples{ 31 | ## There are paths to resource data for each set of files at Inparanoid. 32 | ## This is how you can turn those files inta sqlite DB. 33 | if(interactive()){ 34 | db <- makeInpDb( 35 | dir="http://inparanoid.sbc.su.se/download/current/Orthologs/A.aegypti/", 36 | dataDir=tempdir()) 37 | } 38 | } 39 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/ARABIDOPSIS.DB/man/ARACYC.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@ARACYC} 2 | \alias{@ANNOBJPREFIX@ARACYC} 3 | \title{Mappings between TAIR identifiers and KEGG pathway identifiers} 4 | \description{ 5 | AraCyc \url{http://www.arabidopsis.org/tools/aracyc/} maintains pathway data 6 | for Arabidopsis thaliana. @ANNOBJPREFIX@ARACYC maps TAIR identifiers to the 7 | common names of the pathways in which the genes represented 8 | by the tair identifiers are involved. Information is obtained from 9 | AraCyc. 10 | } 11 | 12 | \details{ 13 | Annotation based on data provided by: @ARACYCSOURCE@ 14 | } 15 | 16 | \references{ 17 | \url{http://www.genome.ad.jp/kegg/} 18 | } 19 | 20 | \seealso{ 21 | \itemize{ 22 | \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of 23 | the \code{select()} interface. 24 | } 25 | } 26 | 27 | \examples{ 28 | ## select() interface: 29 | ## Objects in this package can be accessed using the select() interface 30 | ## from the AnnotationDbi package. See ?select for details. 31 | 32 | ## Bimap interface: 33 | x <- @ANNOBJPREFIX@ARACYC 34 | # Get the tair identifiers that are mapped to pathways 35 | mapped_tairs <- mappedkeys(x) 36 | # Convert to a list 37 | xx <- as.list(x[mapped_tairs]) 38 | if(length(xx) > 0) { 39 | # Get the pathways for the first five tairs 40 | xx[1:5] 41 | # For the first tair 42 | xx[[1]] 43 | } 44 | } 45 | 46 | \keyword{datasets} 47 | 48 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/KEGG.DB/man/ENZYMEID2GO.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@ENZYMEID2GO} 2 | \alias{@ANNOBJPREFIX@ENZYMEID2GO} 3 | \title{An annotation data object that maps Enzyme Commission numbers to 4 | Gene Ontology identifiers} 5 | \description{ 6 | @ANNOBJPREFIX@ENZYMEID2GO maps Enzyme Commission numbers to Gene Ontoloty 7 | (GO) identifiers 8 | } 9 | 10 | \details{ 11 | This is an R object containing key and value pairs. Keys are 12 | Enzyme Commission numbers and values are GO identifiers. Values are vectors of 13 | length 1. Enzyme Commission numbers that can not be mapped to a GO 14 | term are assigned a value NA. 15 | 16 | Mappings were based on data provided by: @ENZYMEID2GOSOURCE@ 17 | } 18 | 19 | \references{ 20 | \url{ftp://ftp.genome.ad.jp/pub/kegg/pathways} 21 | } 22 | 23 | \seealso{ 24 | \itemize{ 25 | \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of 26 | the \code{select()} interface. 27 | } 28 | } 29 | 30 | \examples{ 31 | ## select() interface: 32 | ## Objects in this package can be accessed using the select() interface 33 | ## from the AnnotationDbi package. See ?select for details. 34 | 35 | ## Bimap interface: 36 | xx <- as.list(@ANNOBJPREFIX@ENZYMEID2GO) 37 | if(length(xx) > 0){ 38 | # Get the value of the first key 39 | xx[[1]] 40 | # Get values for a few keys 41 | if(length(xx) >= 3) 42 | xx[1:3] 43 | } 44 | } 45 | \keyword{datasets} 46 | 47 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/ARABIDOPSISCHIP.DB/man/ARACYC.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@ARACYC} 2 | \alias{@ANNOBJPREFIX@ARACYC} 3 | \title{Mappings between probe identifiers and KEGG pathway identifiers} 4 | \description{ 5 | AraCyc \url{http://www.arabidopsis.org/tools/aracyc/} maintains pathway data 6 | for Arabidopsis thaliana. @ANNOBJPREFIX@ARACYC maps probe identifiers to the 7 | common names of the pathways in which the genes represented 8 | by the probe identifiers are involved. Information is obtained from 9 | AraCyc. 10 | } 11 | 12 | \details{ 13 | Annotation based on data provided by: @ARACYCSOURCE@ 14 | } 15 | 16 | \references{ 17 | \url{http://www.genome.ad.jp/kegg/} 18 | } 19 | 20 | \seealso{ 21 | \itemize{ 22 | \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of 23 | the \code{select()} interface. 24 | } 25 | } 26 | 27 | \examples{ 28 | ## select() interface: 29 | ## Objects in this package can be accessed using the select() interface 30 | ## from the AnnotationDbi package. See ?select for details. 31 | 32 | ## Bimap interface: 33 | x <- @ANNOBJPREFIX@ARACYC 34 | # Get the probe identifiers that are mapped to pathways 35 | mapped_probes <- mappedkeys(x) 36 | # Convert to a list 37 | xx <- as.list(x[mapped_probes]) 38 | if(length(xx) > 0) { 39 | # Get the pathways for the first five probes 40 | xx[1:5] 41 | # For the first probe 42 | xx[[1]] 43 | } 44 | } 45 | 46 | \keyword{datasets} 47 | 48 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/ORTHOLOGY.DB/R/zzz.R: -------------------------------------------------------------------------------- 1 | datacache <- new.env(hash=TRUE, parent=emptyenv()) 2 | 3 | @ANNOBJPREFIX@ <- function() showQCData("@ANNOBJPREFIX@", datacache) 4 | @ANNOBJPREFIX@_dbconn <- function() dbconn(datacache) 5 | @ANNOBJPREFIX@_dbfile <- function() dbfile(datacache) 6 | @ANNOBJPREFIX@_dbschema <- function(file="", show.indices=FALSE) dbschema(datacache, file=file, show.indices=show.indices) 7 | @ANNOBJPREFIX@_dbInfo <- function() dbInfo(datacache) 8 | 9 | 10 | .onLoad <- function(libname, pkgname) 11 | { 12 | ## Connect to the SQLite DB 13 | dbfile <- system.file("extdata", "@DBFILE@", package=pkgname, lib.loc=libname) 14 | assign("dbfile", dbfile, envir=datacache) 15 | dbconn <- dbFileConnect(dbfile) 16 | assign("dbconn", dbconn, envir=datacache) 17 | 18 | ## Create the OrgDb object 19 | sPkgname <- sub(".db$","",pkgname) 20 | txdb <- loadDb(system.file("extdata", paste(sPkgname, 21 | ".sqlite",sep=""), package=pkgname, lib.loc=libname), 22 | packageName=pkgname) 23 | dbNewname <- AnnotationDbi:::dbObjectName(pkgname,"OrthologyDb") 24 | ns <- asNamespace(pkgname) 25 | assign(dbNewname, txdb, envir=ns) 26 | namespaceExport(ns, dbNewname) 27 | 28 | 29 | packageStartupMessage(AnnotationDbi:::annoStartupMessages("@ANNOBJPREFIX@")) 30 | } 31 | 32 | .onUnload <- function(libpath) 33 | { 34 | dbFileDisconnect(@ANNOBJPREFIX@_dbconn()) 35 | } 36 | 37 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/ARABIDOPSIS.DB/man/ARACYCENZYME.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@ARACYCENZYME} 2 | \alias{@ANNOBJPREFIX@ARACYCENZYME} 3 | \title{Map between TAIR IDs and Enzyme Names from ARACYC} 4 | \description{ 5 | @ANNOBJPREFIX@ARACYCENZYME is an R object that provides mappings between 6 | TAIR identifiers and Enzyme Names from ARACYC. 7 | } 8 | 9 | \details{ 10 | Each TAIR identifier maps to a named vector containing the 11 | Enzyme name for that gene according to the ARACYC database. If this 12 | information is unknown, the vector will contain an \code{NA}. 13 | 14 | Mappings between tair identifiers and enzyme identifiers were obtained using files 15 | provided by: @ENZYMESOURCE@ 16 | } 17 | 18 | \seealso{ 19 | \itemize{ 20 | \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of 21 | the \code{select()} interface. 22 | } 23 | } 24 | 25 | \examples{ 26 | ## select() interface: 27 | ## Objects in this package can be accessed using the select() interface 28 | ## from the AnnotationDbi package. See ?select for details. 29 | 30 | ## Bimap interface: 31 | x <- @ANNOBJPREFIX@ARACYCENZYME 32 | # Get the tair identifiers that are mapped to an Enzyme Name 33 | mapped_tairs <- mappedkeys(x) 34 | # Convert to a list 35 | xx <- as.list(x[mapped_tairs]) 36 | if(length(xx) > 0) { 37 | # Get the ENZYME name for the first five tairs 38 | xx[1:5] 39 | # Get the first one 40 | xx[[1]] 41 | } 42 | } 43 | \keyword{datasets} 44 | 45 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/NCBICHIP.DB/man/UNIPROT.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@UNIPROT} 2 | \alias{@ANNOBJPREFIX@UNIPROT} 3 | \alias{@ANNOBJPREFIX@UNIPROT2PROBE} 4 | \title{Map Uniprot accession numbers with Entrez Gene identifiers} 5 | \description{ 6 | @ANNOBJPREFIX@UNIPROT is an R object that contains mappings between 7 | the manufacturer identifiers and Uniprot accession numbers. 8 | } 9 | \details{ 10 | This object is a simple mapping of manufacturer identifiers to Uniprot 11 | Accessions. 12 | 13 | Mappings were based on data provided by NCBI (link above) with an 14 | exception for fly, which required retrieving the data from ensembl 15 | \url{http://www.ensembl.org/biomart/martview/} 16 | } 17 | 18 | \seealso{ 19 | \itemize{ 20 | \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of 21 | the \code{select()} interface. 22 | } 23 | } 24 | 25 | \examples{ 26 | ## select() interface: 27 | ## Objects in this package can be accessed using the select() interface 28 | ## from the AnnotationDbi package. See ?select for details. 29 | 30 | ## Bimap interface: 31 | x <- @ANNOBJPREFIX@UNIPROT 32 | # Get the entrez gene IDs that are mapped to an Uniprot ID 33 | mapped_genes <- mappedkeys(x) 34 | # Convert to a list 35 | xx <- as.list(x[mapped_genes][1:300]) 36 | if(length(xx) > 0) { 37 | # Get the Uniprot IDs for the first five genes 38 | xx[1:5] 39 | # Get the first one 40 | xx[[1]] 41 | } 42 | } 43 | \keyword{datasets} 44 | 45 | 46 | 47 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/NOSCHEMA.DB/R/zzz.R: -------------------------------------------------------------------------------- 1 | datacache <- new.env(hash=TRUE, parent=emptyenv()) 2 | 3 | @ANNOBJPREFIX@ <- function() showQCData("@ANNOBJPREFIX@", datacache) 4 | @ANNOBJPREFIX@_dbconn <- function() dbconn(datacache) 5 | @ANNOBJPREFIX@_dbfile <- function() dbfile(datacache) 6 | @ANNOBJPREFIX@_dbschema <- function(file="", show.indices=FALSE) dbschema(datacache, file=file, show.indices=show.indices) 7 | @ANNOBJPREFIX@_dbInfo <- function() dbInfo(datacache) 8 | 9 | @ANNOBJPREFIX@ORGANISM <- "@ORGANISM@" 10 | 11 | .onLoad <- function(libname, pkgname) 12 | { 13 | ## Connect to the SQLite DB 14 | dbfile <- system.file("extdata", "@DBFILE@", package=pkgname, lib.loc=libname) 15 | assign("dbfile", dbfile, envir=datacache) 16 | dbconn <- dbFileConnect(dbfile) 17 | assign("dbconn", dbconn, envir=datacache) 18 | 19 | ## Create the OrgDb object 20 | sPkgname <- sub(".db$","",pkgname) 21 | db <- loadDb(system.file("extdata", paste(sPkgname, 22 | ".sqlite",sep=""), package=pkgname, lib.loc=libname), 23 | packageName=pkgname) 24 | dbNewname <- AnnotationDbi:::dbObjectName(pkgname,"OrgDb") 25 | ns <- asNamespace(pkgname) 26 | assign(dbNewname, db, envir=ns) 27 | namespaceExport(ns, dbNewname) 28 | 29 | packageStartupMessage(AnnotationDbi:::annoStartupMessages("@ANNOBJPREFIX@.db")) 30 | } 31 | 32 | .onUnload <- function(libpath) 33 | { 34 | dbFileDisconnect(@ANNOBJPREFIX@_dbconn()) 35 | } 36 | 37 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/ARABIDOPSIS.DB/man/CHR.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@CHR} 2 | \alias{@ANNOBJPREFIX@CHR} 3 | \title{Map TAIR IDs to Chromosomes} 4 | \description{ 5 | @ANNOBJPREFIX@CHR is an R object that provides mappings between a 6 | TAIR identifier and the chromosome that contains the gene of interest. 7 | } 8 | \details{ 9 | Each TAIR identifier maps to a vector of chromosomes. Due to 10 | inconsistencies that may exist at the time the object was built, 11 | the vector may contain more than one chromosome (e.g., the identifier may map 12 | to more than one chromosome). If the chromosomal location is unknown, 13 | the vector will contain an \code{NA}. 14 | 15 | Mappings were based on data provided by: @CHRSOURCE@ 16 | 17 | } 18 | 19 | \seealso{ 20 | \itemize{ 21 | \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of 22 | the \code{select()} interface. 23 | } 24 | } 25 | 26 | \examples{ 27 | ## select() interface: 28 | ## Objects in this package can be accessed using the select() interface 29 | ## from the AnnotationDbi package. See ?select for details. 30 | 31 | ## Bimap interface: 32 | x <- @ANNOBJPREFIX@CHR 33 | # Get the tair identifiers that are mapped to a chromosome 34 | mapped_tairs <- mappedkeys(x) 35 | # Convert to a list 36 | xx <- as.list(x[mapped_tairs]) 37 | if(length(xx) > 0) { 38 | # Get the CHR for the first five tairs 39 | xx[1:5] 40 | # Get the first one 41 | xx[[1]] 42 | } 43 | } 44 | \keyword{datasets} 45 | 46 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/NCBICHIP.DB/man/ACCNUM.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@ACCNUM} 2 | \alias{@ANNOBJPREFIX@ACCNUM} 3 | \title{Map Manufacturer identifiers to Accession Numbers} 4 | \description{ 5 | @ANNOBJPREFIX@ACCNUM is an R object that contains mappings between a 6 | manufacturer's identifiers and manufacturers accessions. 7 | } 8 | \details{ 9 | For chip packages such as this, the ACCNUM mapping comes directly from the 10 | manufacturer. This is different from other mappings which are mapped onto 11 | the probes via an Entrez Gene identifier. 12 | 13 | Each manufacturer identifier maps to a vector containing a GenBank accession 14 | number. 15 | 16 | Mappings were based on data provided by: @ACCNUMSOURCE@ 17 | } 18 | 19 | \seealso{ 20 | \itemize{ 21 | \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of 22 | the \code{select()} interface. 23 | } 24 | } 25 | 26 | \examples{ 27 | ## select() interface: 28 | ## Objects in this package can be accessed using the select() interface 29 | ## from the AnnotationDbi package. See ?select for details. 30 | 31 | ## Bimap interface: 32 | x <- @ANNOBJPREFIX@ACCNUM 33 | # Get the probe identifiers that are mapped to an ACCNUM 34 | mapped_probes <- mappedkeys(x) 35 | # Convert to a list 36 | xx <- as.list(x[mapped_probes][1:300]) 37 | if(length(xx) > 0) { 38 | # Get the ACCNUM for the first five probes 39 | xx[1:5] 40 | # Get the first one 41 | xx[[1]] 42 | } 43 | } 44 | \keyword{datasets} 45 | 46 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/ARABIDOPSISCHIP.DB/man/ARACYCENZYME.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@ARACYCENZYME} 2 | \alias{@ANNOBJPREFIX@ARACYCENZYME} 3 | \title{Map between Manufacturer IDs and Enzyme Names from ARACYC} 4 | \description{ 5 | @ANNOBJPREFIX@ARACYCENZYME is an R object that provides mappings between 6 | manufacturer identifiers and Enzyme Names from ARACYC. 7 | } 8 | \details{ 9 | Each manufacturer identifier maps to a named vector containing the 10 | Enzyme name for that gene according to the ARACYC database. If this 11 | information is unknown, the vector will contain an \code{NA}. 12 | 13 | Mappings between probe identifiers and enzyme identifiers were obtained 14 | using files provided by: @ENZYMESOURCE@ 15 | } 16 | 17 | \seealso{ 18 | \itemize{ 19 | \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of 20 | the \code{select()} interface. 21 | } 22 | } 23 | 24 | \examples{ 25 | ## select() interface: 26 | ## Objects in this package can be accessed using the select() interface 27 | ## from the AnnotationDbi package. See ?select for details. 28 | 29 | ## Bimap interface: 30 | x <- @ANNOBJPREFIX@ARACYCENZYME 31 | # Get the probe identifiers that are mapped to an Enzyme Name 32 | mapped_probes <- mappedkeys(x) 33 | # Convert to a list 34 | xx <- as.list(x[mapped_probes]) 35 | if(length(xx) > 0) { 36 | # Get the ENZYME name for the first five probes 37 | xx[1:5] 38 | # Get the first one 39 | xx[[1]] 40 | } 41 | } 42 | \keyword{datasets} 43 | 44 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/INPARANOID.DB/man/BASE.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@.db} 2 | \alias{@ANNOBJPREFIX@.db} 3 | \alias{@ANNOBJPREFIX@} 4 | \title{Bioconductor annotation data package} 5 | \description{ 6 | 7 | Welcome to the @ANNOBJPREFIX@.db annotation Package. The purpose of 8 | this package is to provide detailed information about the 9 | @ANNOBJPREFIX@ platform. Bioconductor attempts to update this package 10 | biannually with the most recently available inparanoid data, but 11 | inparanoid data sources have not historically updated that frequently. 12 | Please check inparanoid to learn more about when they have last 13 | updated their databases. 14 | 15 | Objects in this package are accessed using the \code{select()} interface. 16 | See ?select in the AnnotationDbi package for details. 17 | } 18 | 19 | \seealso{ 20 | \itemize{ 21 | \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of 22 | \code{keys()}, \code{columns()} and \code{select()}. 23 | } 24 | } 25 | 26 | \examples{ 27 | ## select() interface: 28 | ## Objects in this package can be accessed using the select() interface 29 | ## from the AnnotationDbi package. See ?select for details. 30 | columns(@ANNOBJPREFIX@.db) 31 | 32 | ## Bimap interface: 33 | ## The 'old style' of interacting with these objects is manipulation as 34 | ## bimaps. While this approach is still available we strongly encourage the 35 | ## use of select(). 36 | ls("package:@ANNOBJPREFIX@.db") 37 | } 38 | \keyword{datasets} 39 | 40 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/KEGG.DB/man/BASE.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@.db} 2 | \alias{@ANNOBJPREFIX@.db} 3 | \alias{@ANNOBJPREFIX@} 4 | \title{Bioconductor annotation data package} 5 | \description{ 6 | 7 | Welcome to the @ANNOBJPREFIX@.db annotation Package. The purpose of 8 | this package was to provide detailed information about the latest 9 | version of the KEGG pathway databases. But a number of years ago, 10 | KEGG changed their policy about sharing their data and so this package 11 | is no longer allowed to be current. Users who are interested in a 12 | more current pathway data are encouraged to look at the KEGGREST or 13 | reactome.db packages. 14 | 15 | Objects in this package are accessed using the \code{select()} interface. 16 | See ?select in the AnnotationDbi package for details. 17 | } 18 | 19 | \seealso{ 20 | \itemize{ 21 | \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of 22 | \code{keys()}, \code{columns()} and \code{select()}. 23 | } 24 | } 25 | 26 | \examples{ 27 | ## select() interface: 28 | ## Objects in this package can be accessed using the select() interface 29 | ## from the AnnotationDbi package. See ?select for details. 30 | columns(@ANNOBJPREFIX@.db) 31 | 32 | ## Bimap interface: 33 | ## The 'old style' of interacting with these objects is manipulation as 34 | ## bimaps. While this approach is still available we strongly encourage the 35 | ## use of select(). 36 | ls("package:@ANNOBJPREFIX@.db") 37 | } 38 | \keyword{datasets} 39 | 40 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/YEASTCHIP.DB/man/CHR.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@CHR} 2 | \alias{@ANNOBJPREFIX@CHR} 3 | \title{Map Manufacturer IDs to Chromosomes} 4 | \description{ 5 | @ANNOBJPREFIX@CHR is an R object that provides mappings between a 6 | manufacturer identifier and the chromosome that contains the gene of interest. 7 | } 8 | \details{ 9 | Each manufacturer identifier maps to a vector of chromosomes. Due to 10 | inconsistencies that may exist at the time the object was built, 11 | the vector may contain more than one chromosome (e.g., the identifier may map 12 | to more than one chromosome). If the chromosomal location is unknown, 13 | the vector will contain an \code{NA}. 14 | 15 | Mappings were based on data provided by: @CHRSOURCE@ 16 | } 17 | 18 | \seealso{ 19 | \itemize{ 20 | \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of 21 | the \code{select()} interface. 22 | } 23 | } 24 | 25 | \examples{ 26 | ## select() interface: 27 | ## Objects in this package can be accessed using the select() interface 28 | ## from the AnnotationDbi package. See ?select for details. 29 | 30 | ## Bimap interface: 31 | x <- @ANNOBJPREFIX@CHR 32 | # Get the probe identifiers that are mapped to a chromosome 33 | mapped_probes <- mappedkeys(x) 34 | # Convert to a list 35 | xx <- as.list(x[mapped_probes]) 36 | if(length(xx) > 0) { 37 | # Get the CHR for the first five probes 38 | xx[1:5] 39 | # Get the first one 40 | xx[[1]] 41 | } 42 | } 43 | 44 | \keyword{datasets} 45 | 46 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/NCBICHIP.DB/man/CHR.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@CHR} 2 | \alias{@ANNOBJPREFIX@CHR} 3 | \title{Map Manufacturer IDs to Chromosomes} 4 | \description{ 5 | @ANNOBJPREFIX@CHR is an R object that provides mappings between a 6 | manufacturer identifier and the chromosome that contains the gene of interest. 7 | } 8 | 9 | \details{ 10 | Each manufacturer identifier maps to a vector of chromosomes. Due to 11 | inconsistencies that may exist at the time the object was built, 12 | the vector may contain more than one chromosome (e.g., the identifier may map 13 | to more than one chromosome). If the chromosomal location is unknown, 14 | the vector will contain an \code{NA}. 15 | 16 | Mappings were based on data provided by: @CHRSOURCE@ 17 | } 18 | 19 | \seealso{ 20 | \itemize{ 21 | \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of 22 | the \code{select()} interface. 23 | } 24 | } 25 | 26 | \examples{ 27 | ## select() interface: 28 | ## Objects in this package can be accessed using the select() interface 29 | ## from the AnnotationDbi package. See ?select for details. 30 | 31 | ## Bimap interface: 32 | x <- @ANNOBJPREFIX@CHR 33 | # Get the probe identifiers that are mapped to a chromosome 34 | mapped_probes <- mappedkeys(x) 35 | # Convert to a list 36 | xx <- as.list(x[mapped_probes][1:300]) 37 | if(length(xx) > 0) { 38 | # Get the CHR for the first five probes 39 | xx[1:5] 40 | # Get the first one 41 | xx[[1]] 42 | } 43 | } 44 | \keyword{datasets} 45 | 46 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/NCBIORG.DB/man/UNIPROT.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@UNIPROT} 2 | \alias{@ANNOBJPREFIX@UNIPROT} 3 | \title{Map Uniprot accession numbers with Entrez Gene identifiers} 4 | \description{ 5 | @ANNOBJPREFIX@UNIPROT is an R object that contains mappings between 6 | Entrez Gene identifiers and Uniprot accession numbers. 7 | } 8 | 9 | \details{ 10 | This object is a simple mapping of Entrez Gene identifiers 11 | \url{https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene} to Uniprot 12 | Accession Numbers. 13 | 14 | Mappings were based on data provided by NCBI (link above) with an 15 | exception for fly, which required retrieving the data from ensembl 16 | \url{http://www.ensembl.org/biomart/martview/} 17 | } 18 | 19 | \seealso{ 20 | \itemize{ 21 | \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of 22 | the \code{select()} interface. 23 | } 24 | } 25 | 26 | \examples{ 27 | ## select() interface: 28 | ## Objects in this package can be accessed using the select() interface 29 | ## from the AnnotationDbi package. See ?select for details. 30 | 31 | ## Bimap interface: 32 | x <- @ANNOBJPREFIX@UNIPROT 33 | # Get the entrez gene IDs that are mapped to a Uniprot ID 34 | mapped_genes <- mappedkeys(x) 35 | # Convert to a list 36 | xx <- as.list(x[mapped_genes]) 37 | if(length(xx) > 0) { 38 | # Get the Uniprot gene IDs for the first five genes 39 | xx[1:5] 40 | # Get the first one 41 | xx[[1]] 42 | } 43 | } 44 | 45 | \keyword{datasets} 46 | 47 | 48 | 49 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/MALARIA.DB/tests/unit/test.R: -------------------------------------------------------------------------------- 1 | testForGOSourceMismatches <- function(){ 2 | require("GO.db") 3 | require("annotate") 4 | require("@PKGNAME@") 5 | g = Lkeys(GOTERM) 6 | m = Rkeys(getAnnMap('GO2ORF', gsub(".db$","","@PKGNAME@"))) 7 | ##Are all the IDs from m in g? 8 | all((m %in% g)) 9 | } 10 | 11 | msg = paste("The GO annotations are out of sync between the GO.db and the", 12 | " annotation package being tested. Please ensure that GO.db", 13 | " is the very latest version, or update the the relevant", 14 | " .db0 source packages and recreate the package.", sep="") 15 | 16 | checkTrue(testForGOSourceMismatches(), 17 | msg = paste(strwrap(msg, exdent=2),collapse="\n") ) 18 | 19 | getGODate <- function(){ 20 | require(GO.db) 21 | dbmeta(GO_dbconn(), "GOSOURCEDATE") 22 | } 23 | 24 | getPkgDate <-function(){ 25 | require("@PKGNAME@") 26 | dbmeta(eval(call(name = paste(gsub(".db$","","@PKGNAME@"), 27 | "_dbconn",sep=""))), "GOSOURCEDATE") 28 | } 29 | 30 | msg = paste("The date stamps for the GO annotations are out of sync between", 31 | " the GO.db and the annotation package being tested. Please", 32 | " ensure that GO.db is the very latest version, or update to", 33 | " the relevant .db0 source packages to recreate the package.", 34 | sep="") 35 | 36 | checkIdentical(getGODate(), getPkgDate(), 37 | msg = paste(strwrap(msg, exdent=2),collapse="\n") ) 38 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/NCBIORG.DB/tests/unit/test.R: -------------------------------------------------------------------------------- 1 | testForGOSourceMismatches <- function(){ 2 | require("GO.db") 3 | require("annotate") 4 | require("@PKGNAME@") 5 | g = Lkeys(GOTERM) 6 | m = Rkeys(getAnnMap('GO2EG', gsub(".db$","","@PKGNAME@"))) 7 | ##Are all the IDs from m in g? 8 | all((m %in% g)) 9 | } 10 | 11 | msg = paste("The GO annotations are out of sync between the GO.db and the", 12 | " annotation package being tested. Please ensure that GO.db", 13 | " is the very latest version, or update the the relevant", 14 | " .db0 source packages and recreate the package.", sep="") 15 | 16 | checkTrue(testForGOSourceMismatches(), 17 | msg = paste(strwrap(msg, exdent=2),collapse="\n") ) 18 | 19 | getGODate <- function(){ 20 | require(GO.db) 21 | dbmeta(GO_dbconn(), "GOSOURCEDATE") 22 | } 23 | 24 | getPkgDate <-function(){ 25 | require("@PKGNAME@") 26 | dbmeta(eval(call(name = paste(gsub(".db$","","@PKGNAME@"), 27 | "_dbconn",sep=""))), "GOSOURCEDATE") 28 | } 29 | 30 | msg = paste("The date stamps for the GO annotations are out of sync between", 31 | " the GO.db and the annotation package being tested. Please", 32 | " ensure that GO.db is the very latest version, or update to", 33 | " the relevant .db0 source packages to recreate the package.", 34 | sep="") 35 | 36 | checkIdentical(getGODate(), getPkgDate(), 37 | msg = paste(strwrap(msg, exdent=2),collapse="\n") ) 38 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/ORGANISM.DB/tests/unit/test.R: -------------------------------------------------------------------------------- 1 | testForGOSourceMismatches <- function(){ 2 | require("GO.db") 3 | require("annotate") 4 | require("@PKGNAME@") 5 | g = Lkeys(GOTERM) 6 | m = Rkeys(getAnnMap('GO2EG', gsub(".db$","","@PKGNAME@"))) 7 | ##Are all the IDs from m in g? 8 | all((m %in% g)) 9 | } 10 | 11 | msg = paste("The GO annotations are out of sync between the GO.db and the", 12 | " annotation package being tested. Please ensure that GO.db", 13 | " is the very latest version, or update the the relevant", 14 | " .db0 source packages and recreate the package.", sep="") 15 | 16 | checkTrue(testForGOSourceMismatches(), 17 | msg = paste(strwrap(msg, exdent=2),collapse="\n") ) 18 | 19 | getGODate <- function(){ 20 | require(GO.db) 21 | dbmeta(GO_dbconn(), "GOSOURCEDATE") 22 | } 23 | 24 | getPkgDate <-function(){ 25 | require("@PKGNAME@") 26 | dbmeta(eval(call(name = paste(gsub(".db$","","@PKGNAME@"), 27 | "_dbconn",sep=""))), "GOSOURCEDATE") 28 | } 29 | 30 | msg = paste("The date stamps for the GO annotations are out of sync between", 31 | " the GO.db and the annotation package being tested. Please", 32 | " ensure that GO.db is the very latest version, or update to", 33 | " the relevant .db0 source packages to recreate the package.", 34 | sep="") 35 | 36 | checkIdentical(getGODate(), getPkgDate(), 37 | msg = paste(strwrap(msg, exdent=2),collapse="\n") ) 38 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/ORTHOLOGY.DB/tests/unit/test.R: -------------------------------------------------------------------------------- 1 | testForGOSourceMismatches <- function(){ 2 | require("GO.db") 3 | require("annotate") 4 | require("@PKGNAME@") 5 | g = Lkeys(GOTERM) 6 | m = Rkeys(getAnnMap('GO2EG', gsub(".db$","","@PKGNAME@"))) 7 | ##Are all the IDs from m in g? 8 | all((m %in% g)) 9 | } 10 | 11 | msg = paste("The GO annotations are out of sync between the GO.db and the", 12 | " annotation package being tested. Please ensure that GO.db", 13 | " is the very latest version, or update the the relevant", 14 | " .db0 source packages and recreate the package.", sep="") 15 | 16 | checkTrue(testForGOSourceMismatches(), 17 | msg = paste(strwrap(msg, exdent=2),collapse="\n") ) 18 | 19 | getGODate <- function(){ 20 | require(GO.db) 21 | dbmeta(GO_dbconn(), "GOSOURCEDATE") 22 | } 23 | 24 | getPkgDate <-function(){ 25 | require("@PKGNAME@") 26 | dbmeta(eval(call(name = paste(gsub(".db$","","@PKGNAME@"), 27 | "_dbconn",sep=""))), "GOSOURCEDATE") 28 | } 29 | 30 | msg = paste("The date stamps for the GO annotations are out of sync between", 31 | " the GO.db and the annotation package being tested. Please", 32 | " ensure that GO.db is the very latest version, or update to", 33 | " the relevant .db0 source packages to recreate the package.", 34 | sep="") 35 | 36 | checkIdentical(getGODate(), getPkgDate(), 37 | msg = paste(strwrap(msg, exdent=2),collapse="\n") ) 38 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/YEAST.DB/tests/unit/test.R: -------------------------------------------------------------------------------- 1 | testForGOSourceMismatches <- function(){ 2 | require("GO.db") 3 | require("annotate") 4 | require("@PKGNAME@") 5 | g = Lkeys(GOTERM) 6 | m = Rkeys(getAnnMap('GO2ORF', gsub(".db$","","@PKGNAME@"))) 7 | ##Are all the IDs from m in g? 8 | all((m %in% g)) 9 | } 10 | 11 | msg = paste("The GO annotations are out of sync between the GO.db and the", 12 | " annotation package being tested. Please ensure that GO.db", 13 | " is the very latest version, or update the the relevant", 14 | " .db0 source packages and recreate the package.", sep="") 15 | 16 | checkTrue(testForGOSourceMismatches(), 17 | msg = paste(strwrap(msg, exdent=2),collapse="\n") ) 18 | 19 | getGODate <- function(){ 20 | require(GO.db) 21 | dbmeta(GO_dbconn(), "GOSOURCEDATE") 22 | } 23 | 24 | getPkgDate <-function(){ 25 | require("@PKGNAME@") 26 | dbmeta(eval(call(name = paste(gsub(".db$","","@PKGNAME@"), 27 | "_dbconn",sep=""))), "GOSOURCEDATE") 28 | } 29 | 30 | msg = paste("The date stamps for the GO annotations are out of sync between", 31 | " the GO.db and the annotation package being tested. Please", 32 | " ensure that GO.db is the very latest version, or update to", 33 | " the relevant .db0 source packages to recreate the package.", 34 | sep="") 35 | 36 | checkIdentical(getGODate(), getPkgDate(), 37 | msg = paste(strwrap(msg, exdent=2),collapse="\n") ) 38 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/YEASTNCBI.DB/tests/unit/test.R: -------------------------------------------------------------------------------- 1 | testForGOSourceMismatches <- function(){ 2 | require("GO.db") 3 | require("annotate") 4 | require("@PKGNAME@") 5 | g = Lkeys(GOTERM) 6 | m = Rkeys(getAnnMap('GO2EG', gsub(".db$","","@PKGNAME@"))) 7 | ##Are all the IDs from m in g? 8 | all((m %in% g)) 9 | } 10 | 11 | msg = paste("The GO annotations are out of sync between the GO.db and the", 12 | " annotation package being tested. Please ensure that GO.db", 13 | " is the very latest version, or update the the relevant", 14 | " .db0 source packages and recreate the package.", sep="") 15 | 16 | checkTrue(testForGOSourceMismatches(), 17 | msg = paste(strwrap(msg, exdent=2),collapse="\n") ) 18 | 19 | getGODate <- function(){ 20 | require(GO.db) 21 | dbmeta(GO_dbconn(), "GOSOURCEDATE") 22 | } 23 | 24 | getPkgDate <-function(){ 25 | require("@PKGNAME@") 26 | dbmeta(eval(call(name = paste(gsub(".db$","","@PKGNAME@"), 27 | "_dbconn",sep=""))), "GOSOURCEDATE") 28 | } 29 | 30 | msg = paste("The date stamps for the GO annotations are out of sync between", 31 | " the GO.db and the annotation package being tested. Please", 32 | " ensure that GO.db is the very latest version, or update to", 33 | " the relevant .db0 source packages to recreate the package.", 34 | sep="") 35 | 36 | checkIdentical(getGODate(), getPkgDate(), 37 | msg = paste(strwrap(msg, exdent=2),collapse="\n") ) 38 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/ARABIDOPSIS.DB/tests/unit/test.R: -------------------------------------------------------------------------------- 1 | testForGOSourceMismatches <- function(){ 2 | require("GO.db") 3 | require("annotate") 4 | require("@PKGNAME@") 5 | g = Lkeys(GOTERM) 6 | m = Rkeys(getAnnMap('GO2TAIR', gsub(".db$","","@PKGNAME@"))) 7 | ##Are all the IDs from m in g? 8 | all((m %in% g)) 9 | } 10 | 11 | msg = paste("The GO annotations are out of sync between the GO.db and the", 12 | " annotation package being tested. Please ensure that GO.db", 13 | " is the very latest version, or update the the relevant", 14 | " .db0 source packages and recreate the package.", sep="") 15 | 16 | checkTrue(testForGOSourceMismatches(), 17 | msg = paste(strwrap(msg, exdent=2),collapse="\n") ) 18 | 19 | getGODate <- function(){ 20 | require(GO.db) 21 | dbmeta(GO_dbconn(), "GOSOURCEDATE") 22 | } 23 | 24 | getPkgDate <-function(){ 25 | require("@PKGNAME@") 26 | dbmeta(eval(call(name = paste(gsub(".db$","","@PKGNAME@"), 27 | "_dbconn",sep=""))), "GOSOURCEDATE") 28 | } 29 | 30 | msg = paste("The date stamps for the GO annotations are out of sync between", 31 | " the GO.db and the annotation package being tested. Please", 32 | " ensure that GO.db is the very latest version, or update to", 33 | " the relevant .db0 source packages to recreate the package.", 34 | sep="") 35 | 36 | checkIdentical(getGODate(), getPkgDate(), 37 | msg = paste(strwrap(msg, exdent=2),collapse="\n") ) 38 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/ARABIDOPSISCHIP.DB/man/CHR.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@CHR} 2 | \alias{@ANNOBJPREFIX@CHR} 3 | \title{Map Manufacturer IDs to Chromosomes} 4 | \description{ 5 | @ANNOBJPREFIX@CHR is an R object that provides mappings between a 6 | manufacturer identifier and the chromosome that contains the gene of interest. 7 | } 8 | \details{ 9 | Each manufacturer identifier maps to a vector of chromosomes. Due to 10 | inconsistencies that may exist at the time the object was built, 11 | the vector may contain more than one chromosome (e.g., the identifier may map 12 | to more than one chromosome). If the chromosomal location is unknown, 13 | the vector will contain an \code{NA}. 14 | 15 | Mappings were based on data provided by: @CHRSOURCE@ 16 | 17 | } 18 | 19 | \seealso{ 20 | \itemize{ 21 | \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of 22 | the \code{select()} interface. 23 | } 24 | } 25 | 26 | \examples{ 27 | ## select() interface: 28 | ## Objects in this package can be accessed using the select() interface 29 | ## from the AnnotationDbi package. See ?select for details. 30 | 31 | ## Bimap interface: 32 | x <- @ANNOBJPREFIX@CHR 33 | # Get the probe identifiers that are mapped to a chromosome 34 | mapped_probes <- mappedkeys(x) 35 | # Convert to a list 36 | xx <- as.list(x[mapped_probes]) 37 | if(length(xx) > 0) { 38 | # Get the CHR for the first five probes 39 | xx[1:5] 40 | # Get the first one 41 | xx[[1]] 42 | } 43 | } 44 | 45 | \keyword{datasets} 46 | 47 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/COELICOLOR.DB/tests/unit/test.R: -------------------------------------------------------------------------------- 1 | testForGOSourceMismatches <- function(){ 2 | require("GO.db") 3 | require("annotate") 4 | require("@PKGNAME@") 5 | g = Lkeys(GOTERM) 6 | m = Rkeys(getAnnMap('GO2EG', gsub(".db$","","@PKGNAME@"))) 7 | ##Are all the IDs from m in g? 8 | all((m %in% g)) 9 | } 10 | 11 | msg = paste("The GO annotations are out of sync between the GO.db and the", 12 | " annotation package being tested. Please ensure that GO.db", 13 | " is the very latest version, or update the the relevant", 14 | " .db0 source packages and recreate the package.", sep="") 15 | 16 | checkTrue(testForGOSourceMismatches(), 17 | msg = paste(strwrap(msg, exdent=2),collapse="\n") ) 18 | 19 | getGODate <- function(){ 20 | require(GO.db) 21 | dbmeta(GO_dbconn(), "GOSOURCEDATE") 22 | } 23 | 24 | getPkgDate <-function(){ 25 | require("@PKGNAME@") 26 | dbmeta(eval(call(name = paste(gsub(".db$","","@PKGNAME@"), 27 | "_dbconn",sep=""))), "GOSOURCEDATE") 28 | } 29 | 30 | msg = paste("The date stamps for the GO annotations are out of sync between", 31 | " the GO.db and the annotation package being tested. Please", 32 | " ensure that GO.db is the very latest version, or update to", 33 | " the relevant .db0 source packages to recreate the package.", 34 | sep="") 35 | 36 | checkIdentical(getGODate(), getPkgDate(), 37 | msg = paste(strwrap(msg, exdent=2),collapse="\n") ) 38 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/NOCHIPSCHEMA.DB/R/zzz.R: -------------------------------------------------------------------------------- 1 | datacache <- new.env(hash=TRUE, parent=emptyenv()) 2 | 3 | @ANNOBJPREFIX@ <- function() showQCData("@ANNOBJPREFIX@", datacache) 4 | @ANNOBJPREFIX@_dbconn <- function() dbconn(datacache) 5 | @ANNOBJPREFIX@_dbfile <- function() dbfile(datacache) 6 | @ANNOBJPREFIX@_dbschema <- function(file="", show.indices=FALSE) dbschema(datacache, file=file, show.indices=show.indices) 7 | @ANNOBJPREFIX@_dbInfo <- function() dbInfo(datacache) 8 | 9 | @ANNOBJPREFIX@ORGPKG <- "@ORGPKGDEP@" 10 | @ANNOBJPREFIX@ORGANISM <- "@ORGANISM@" 11 | 12 | .onLoad <- function(libname, pkgname) 13 | { 14 | ## Connect to the SQLite DB 15 | dbfile <- system.file("extdata", "@DBFILE@", package=pkgname, lib.loc=libname) 16 | assign("dbfile", dbfile, envir=datacache) 17 | dbconn <- dbFileConnect(dbfile) 18 | assign("dbconn", dbconn, envir=datacache) 19 | 20 | ## Create the OrgDb object 21 | sPkgname <- sub(".db$","",pkgname) 22 | db <- loadDb(system.file("extdata", paste(sPkgname, 23 | ".sqlite",sep=""), package=pkgname, lib.loc=libname), 24 | packageName=pkgname) 25 | dbNewname <- AnnotationDbi:::dbObjectName(pkgname,"ChipDb") 26 | ns <- asNamespace(pkgname) 27 | assign(dbNewname, db, envir=ns) 28 | namespaceExport(ns, dbNewname) 29 | 30 | packageStartupMessage(AnnotationDbi:::annoStartupMessages("@ANNOBJPREFIX@.db")) 31 | } 32 | 33 | .onUnload <- function(libpath) 34 | { 35 | dbFileDisconnect(@ANNOBJPREFIX@_dbconn()) 36 | } 37 | 38 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/YEAST.DB/man/ALIAS.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@ALIAS} 2 | \alias{@ANNOBJPREFIX@ALIAS} 3 | \alias{@ANNOBJPREFIX@ALIAS2ORF} 4 | \title{Map Open Reading Frame (ORF) Identifiers to Alias Gene Names} 5 | \description{ 6 | A set of gene names may have been used to report yeast genes 7 | represented by ORF identifiers. One of these names is chosen to be the primary 8 | gene name, and the others are considered aliases. This R object 9 | provides mappings between the primary name and aliases. 10 | } 11 | \details{ 12 | Each primary name maps to a vector of alias names. If there are no 13 | aliases, the vector will contain \code{NA}. 14 | 15 | Annotation based on data provided by: @ALIASSOURCE@ 16 | } 17 | 18 | \references{ 19 | \url{http://www.yeastgenome.org/DownloadContents.shtml} 20 | } 21 | 22 | \seealso{ 23 | \itemize{ 24 | \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of 25 | the \code{select()} interface. 26 | } 27 | } 28 | 29 | \examples{ 30 | ## select() interface: 31 | ## Objects in this package can be accessed using the select() interface 32 | ## from the AnnotationDbi package. See ?select for details. 33 | 34 | ## Bimap interface: 35 | x <- @ANNOBJPREFIX@ALIAS 36 | # Get the probe identifiers that are mapped to alias names 37 | mapped_probes <- mappedkeys(x) 38 | # Convert to a list 39 | xx <- as.list(x[mapped_probes]) 40 | if(length(xx) > 0) { 41 | # Get the alias names for the first five probes 42 | xx[1:5] 43 | # For the first probe 44 | xx[[1]] 45 | } 46 | } 47 | \keyword{datasets} 48 | 49 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/YEAST.DB/man/GENENAME.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@GENENAME} 2 | \alias{@ANNOBJPREFIX@GENENAME} 3 | \title{Map between ORF IDs and Genes} 4 | \description{ 5 | @ANNOBJPREFIX@GENENAME is an R object that maps ORF 6 | identifiers to the corresponding gene name. 7 | } 8 | \details{ 9 | Each ORF identifier maps to a named vector containing the gene 10 | name. The vector name corresponds to the ORF identifier. If the 11 | gene name is unknown, the vector will contain an \code{NA}. 12 | 13 | Gene names currently include both the official (validated by a 14 | nomenclature committee) and preferred names (interim selected for 15 | display) for genes. Efforts are being made to differentiate the two 16 | by adding a name to the vector. 17 | 18 | Mappings were based on data provided by: @GENENAMESOURCE@ 19 | } 20 | 21 | \seealso{ 22 | \itemize{ 23 | \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of 24 | the \code{select()} interface. 25 | } 26 | } 27 | 28 | \examples{ 29 | ## select() interface: 30 | ## Objects in this package can be accessed using the select() interface 31 | ## from the AnnotationDbi package. See ?select for details. 32 | 33 | ## Bimap interface: 34 | x <- @ANNOBJPREFIX@GENENAME 35 | # Get the gene names that are mapped to an ORF identifier 36 | mapped_genes <- mappedkeys(x) 37 | # Convert to a list 38 | xx <- as.list(x[mapped_genes]) 39 | if(length(xx) > 0) { 40 | # Get the GENE NAME for the first five genes 41 | xx[1:5] 42 | # Get the first one 43 | xx[[1]] 44 | } 45 | } 46 | \keyword{datasets} 47 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/YEASTCHIP.DB/man/ALIAS.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@ALIAS} 2 | \alias{@ANNOBJPREFIX@ALIAS} 3 | \alias{@ANNOBJPREFIX@ALIAS2PROBE} 4 | \title{Map Open Reading Frame (ORF) Identifiers to Alias Gene Names} 5 | \description{ 6 | A set of gene names may have been used to report yeast genes 7 | represented by ORF identifiers. One of these names is chosen to be the primary 8 | gene name, and the others are considered aliases. This R object 9 | provides mappings between the primary name and aliases. 10 | } 11 | \details{ 12 | Each primary name maps to a vector of alias names. If there are no 13 | aliases, the vector will contain \code{NA}. 14 | 15 | Annotation based on data provided by: @ALIASSOURCE@ 16 | } 17 | 18 | \references{ 19 | \url{http://www.yeastgenome.org/DownloadContents.shtml} 20 | } 21 | 22 | \seealso{ 23 | \itemize{ 24 | \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of 25 | the \code{select()} interface. 26 | } 27 | } 28 | 29 | \examples{ 30 | ## select() interface: 31 | ## Objects in this package can be accessed using the select() interface 32 | ## from the AnnotationDbi package. See ?select for details. 33 | 34 | ## Bimap interface: 35 | x <- @ANNOBJPREFIX@ALIAS 36 | # Get the probe identifiers that are mapped to alias names 37 | mapped_probes <- mappedkeys(x) 38 | # Convert to a list 39 | xx <- as.list(x[mapped_probes]) 40 | if(length(xx) > 0) { 41 | # Get the alias names for the first five probes 42 | xx[1:5] 43 | # For the first probe 44 | xx[[1]] 45 | } 46 | } 47 | 48 | \keyword{datasets} 49 | 50 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/YEASTCHIP.DB/man/ORF.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@ORF} 2 | \alias{@ANNOBJPREFIX@ORF} 3 | \title{Map Manufacturer Identifiers to Open Reading Frame (ORF) Identifiers} 4 | \description{ 5 | @ANNOBJPREFIX@ORF is an R object that provides mappings between 6 | manufacturer and ORF identifiers. 7 | } 8 | \details{ 9 | Each manufacturer identifier is mapped to a vector of ORF identifiers. The length of 10 | the vector may be one or longer, depending on how many ORF identifiers the 11 | manufacturer identifier can be mapped to. An \code{NA} is reported for any 12 | manufacturer identifier that cannot be mapped to an ORF identifier at this time. 13 | 14 | Annotation based on data provided by: @ORFSOURCE@ 15 | 16 | } 17 | 18 | \references{ 19 | \url{http://www.yeastgenome.org/DownloadContents.shtml} 20 | } 21 | 22 | \seealso{ 23 | \itemize{ 24 | \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of 25 | the \code{select()} interface. 26 | } 27 | } 28 | 29 | \examples{ 30 | ## select() interface: 31 | ## Objects in this package can be accessed using the select() interface 32 | ## from the AnnotationDbi package. See ?select for details. 33 | 34 | ## Bimap interface: 35 | x <- @ANNOBJPREFIX@ORF 36 | # Get the probe identifiers that are mapped to ORF identifiers 37 | mapped_probes <- mappedkeys(x) 38 | # Convert to a list 39 | xx <- as.list(x[mapped_probes]) 40 | if(length(xx) > 0) { 41 | # Get the ORF identifiers for the first five probes 42 | xx[1:5] 43 | # For the first probe 44 | xx[[1]] 45 | } 46 | } 47 | \keyword{datasets} 48 | 49 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/MALARIA.DB/man/GENENAME.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@GENENAME} 2 | \alias{@ANNOBJPREFIX@GENENAME} 3 | \title{Map between ORF IDs and Genes} 4 | \description{ 5 | @ANNOBJPREFIX@GENENAME is an R object that maps ORF 6 | identifiers to the corresponding gene name. 7 | } 8 | \details{ 9 | Each ORF identifier maps to a named vector containing the gene 10 | name. The vector name corresponds to the ORF identifier. If the 11 | gene name is unknown, the vector will contain an \code{NA}. 12 | 13 | Gene names currently include both the official (validated by a 14 | nomenclature committee) and preferred names (interim selected for 15 | display) for genes. Efforts are being made to differentiate the two 16 | by adding a name to the vector. 17 | 18 | Mappings were based on data provided by: @GENENAMESOURCE@ 19 | 20 | } 21 | 22 | \seealso{ 23 | \itemize{ 24 | \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of 25 | the \code{select()} interface. 26 | } 27 | } 28 | 29 | \examples{ 30 | ## select() interface: 31 | ## Objects in this package can be accessed using the select() interface 32 | ## from the AnnotationDbi package. See ?select for details. 33 | 34 | ## Bimap interface: 35 | x <- @ANNOBJPREFIX@GENENAME 36 | # Get the gene names that are mapped to an ORF identifier 37 | mapped_genes <- mappedkeys(x) 38 | # Convert to a list 39 | xx <- as.list(x[mapped_genes]) 40 | if(length(xx) > 0) { 41 | # Get the GENE NAME for the first five genes 42 | xx[1:5] 43 | # Get the first one 44 | xx[[1]] 45 | } 46 | } 47 | \keyword{datasets} 48 | 49 | 50 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/NCBICHIP.DB/man/FLYBASE.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@FLYBASE} 2 | \alias{@ANNOBJPREFIX@FLYBASE} 3 | \alias{@ANNOBJPREFIX@FLYBASE2PROBE} 4 | \title{Map manufacturer identifiers with FlyBase Acession numbers} 5 | \description{ 6 | @ANNOBJPREFIX@FLYBASE is an R object that contains mappings between 7 | manufacturer identifiers and FlyBase accession numbers. 8 | } 9 | \details{ 10 | This object is a simple mapping of manufacturer identifiers to Flybase 11 | Accession Numbers. 12 | 13 | Mappings were based on data provided by: @FLYBASESOURCE@ 14 | } 15 | 16 | \seealso{ 17 | \itemize{ 18 | \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of 19 | the \code{select()} interface. 20 | } 21 | } 22 | 23 | \examples{ 24 | ## select() interface: 25 | ## Objects in this package can be accessed using the select() interface 26 | ## from the AnnotationDbi package. See ?select for details. 27 | 28 | ## Bimap interface: 29 | x <- @ANNOBJPREFIX@FLYBASE 30 | # Get the manufacturer identifiers that are mapped to a FLYBASE ID 31 | mapped_genes <- mappedkeys(x) 32 | # Convert to a list 33 | xx <- as.list(x[mapped_genes]) 34 | if(length(xx) > 0) { 35 | # Get the FlyBase IDs for the first five genes 36 | xx[1:5] 37 | # Get the first one 38 | xx[[1]] 39 | } 40 | # For the reverse map: 41 | # Convert to a list 42 | xx <- as.list(@ANNOBJPREFIX@FLYBASE2PROBE) 43 | if(length(xx) > 0){ 44 | # Get the probe identifiers for the first five IDs 45 | xx[1:5] 46 | # Get the first one 47 | xx[[1]] 48 | } 49 | } 50 | 51 | \keyword{datasets} 52 | 53 | 54 | 55 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/YEASTNCBI.DB/man/ORF.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@ORF} 2 | \alias{@ANNOBJPREFIX@ORF} 3 | \alias{@ANNOBJPREFIX@ORF2EG} 4 | \title{Map ORF acessions with Entrez Gene identifiers} 5 | \description{ 6 | @ANNOBJPREFIX@ORF is an R object that contains mappings between 7 | Entrez Gene identifiers and ORF accessions. 8 | } 9 | 10 | \details{ 11 | This object is a simple mapping of Entrez Gene identifiers 12 | \url{https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene} to ORF 13 | accessions. 14 | 15 | Mappings were based on data provided by: @ORFSOURCE@ 16 | } 17 | 18 | \seealso{ 19 | \itemize{ 20 | \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of 21 | the \code{select()} interface. 22 | } 23 | } 24 | 25 | \examples{ 26 | ## select() interface: 27 | ## Objects in this package can be accessed using the select() interface 28 | ## from the AnnotationDbi package. See ?select for details. 29 | 30 | ## Bimap interface: 31 | x <- @ANNOBJPREFIX@ORF 32 | # Get the entrez gene identifiers that are mapped to a ORF ID 33 | mapped_genes <- mappedkeys(x) 34 | # Convert to a list 35 | xx <- as.list(x[mapped_genes]) 36 | if(length(xx) > 0) { 37 | # Get the Orf IDs for the first five genes 38 | xx[1:5] 39 | # Get the first one 40 | xx[[1]] 41 | } 42 | #For the reverse map ORF2EG: 43 | # Convert to a list 44 | xx <- as.list(@ANNOBJPREFIX@ORF2EG) 45 | if(length(xx) > 0){ 46 | # Gets the entrez gene identifiers for the first five ORF IDs 47 | xx[1:5] 48 | # Get the first one 49 | xx[[1]] 50 | } 51 | } 52 | \keyword{datasets} 53 | 54 | 55 | 56 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/ARABIDOPSIS.DB/man/GENENAME.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@GENENAME} 2 | \alias{@ANNOBJPREFIX@GENENAME} 3 | \title{Map between TAIR IDs and Genes} 4 | \description{ 5 | @ANNOBJPREFIX@GENENAME is an R object that maps TAIR 6 | identifiers to the corresponding gene name. 7 | } 8 | 9 | \details{ 10 | Each TAIR identifier maps to a named vector containing the gene 11 | name. The vector name corresponds to the TAIR identifier. If 12 | the gene name is unknown, the vector will contain an \code{NA}. 13 | 14 | Gene names currently include both the official (validated by a 15 | nomenclature committee) and preferred names (interim selected for 16 | display) for genes. Efforts are being made to differentiate the two 17 | by adding a name to the vector. 18 | 19 | Mappings were based on data provided by: @GENENAMESOURCE@ 20 | 21 | } 22 | 23 | \seealso{ 24 | \itemize{ 25 | \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of 26 | the \code{select()} interface. 27 | } 28 | } 29 | 30 | \examples{ 31 | ## select() interface: 32 | ## Objects in this package can be accessed using the select() interface 33 | ## from the AnnotationDbi package. See ?select for details. 34 | 35 | ## Bimap interface: 36 | x <- @ANNOBJPREFIX@GENENAME 37 | # Get the TAIR identifiers that are mapped to a gene name 38 | mapped_tairs <- mappedkeys(x) 39 | # Convert to a list 40 | xx <- as.list(x[mapped_tairs]) 41 | if(length(xx) > 0) { 42 | # Get the GENENAME for the first five tairs 43 | xx[1:5] 44 | # Get the first one 45 | xx[[1]] 46 | } 47 | } 48 | \keyword{datasets} 49 | 50 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/YEASTNCBI.DB/man/SGD.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@SGD} 2 | \alias{@ANNOBJPREFIX@SGD} 3 | \alias{@ANNOBJPREFIX@SGD2EG} 4 | \title{Map SGD acession numbers with Entrez Gene identifiers} 5 | \description{ 6 | @ANNOBJPREFIX@SGD is an R object that contains mappings between 7 | Entrez Gene identifiers and SGD accession numbers. 8 | } 9 | \details{ 10 | This object is a simple mapping of Entrez Gene identifiers 11 | \url{https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene} to SGD 12 | accession numbers. 13 | 14 | Mappings were based on data provided by: @SGDSOURCE@ 15 | } 16 | 17 | \seealso{ 18 | \itemize{ 19 | \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of 20 | the \code{select()} interface. 21 | } 22 | } 23 | 24 | \examples{ 25 | ## select() interface: 26 | ## Objects in this package can be accessed using the select() interface 27 | ## from the AnnotationDbi package. See ?select for details. 28 | 29 | ## Bimap interface: 30 | x <- @ANNOBJPREFIX@SGD 31 | # Get the entrez gene identifiers that are mapped to a SGD ID 32 | mapped_genes <- mappedkeys(x) 33 | # Convert to a list 34 | xx <- as.list(x[mapped_genes]) 35 | if(length(xx) > 0) { 36 | # Get the Sgd IDs for the first five genes 37 | xx[1:5] 38 | # Get the first one 39 | xx[[1]] 40 | } 41 | #For the reverse map SGD2EG: 42 | # Convert to a list 43 | xx <- as.list(@ANNOBJPREFIX@SGD2EG) 44 | if(length(xx) > 0){ 45 | # Gets the entrez gene identifiers for the first five SGD IDs 46 | xx[1:5] 47 | # Get the first one 48 | xx[[1]] 49 | } 50 | } 51 | \keyword{datasets} 52 | 53 | 54 | 55 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/GO.DB/R/zzz.R: -------------------------------------------------------------------------------- 1 | datacache <- new.env(hash=TRUE, parent=emptyenv()) 2 | 3 | @ANNOBJPREFIX@ <- function() showQCData("@ANNOBJPREFIX@", datacache) 4 | @ANNOBJPREFIX@_dbconn <- function() dbconn(datacache) 5 | @ANNOBJPREFIX@_dbfile <- function() dbfile(datacache) 6 | @ANNOBJPREFIX@_dbschema <- function(file="", show.indices=FALSE) dbschema(datacache, file=file, show.indices=show.indices) 7 | @ANNOBJPREFIX@_dbInfo <- function() dbInfo(datacache) 8 | 9 | .onLoad <- function(libname, pkgname) 10 | { 11 | ## Connect to the SQLite DB 12 | dbfile <- system.file("extdata", "@DBFILE@", package=pkgname, lib.loc=libname) 13 | assign("dbfile", dbfile, envir=datacache) 14 | dbconn <- dbFileConnect(dbfile) 15 | assign("dbconn", dbconn, envir=datacache) 16 | 17 | ## Create the OrgDb object 18 | sPkgname <- sub(".db$","",pkgname) 19 | txdb <- loadDb(system.file("extdata", paste(sPkgname, 20 | ".sqlite",sep=""), package=pkgname, lib.loc=libname), 21 | packageName=pkgname) 22 | dbNewname <- AnnotationDbi:::dbObjectName(pkgname,"GODb") 23 | ns <- asNamespace(pkgname) 24 | assign(dbNewname, txdb, envir=ns) 25 | namespaceExport(ns, dbNewname) 26 | 27 | ## Create the AnnObj instances 28 | ann_objs <- createAnnObjs.SchemaChoice("@DBSCHEMA@", "@ANNOBJPREFIX@", "@ANNOBJTARGET@", dbconn, datacache) 29 | mergeToNamespaceAndExport(ann_objs, pkgname) 30 | packageStartupMessage(AnnotationDbi:::annoStartupMessages("@ANNOBJPREFIX@.db")) 31 | } 32 | 33 | .onUnload <- function(libpath) 34 | { 35 | dbFileDisconnect(@ANNOBJPREFIX@_dbconn()) 36 | } 37 | 38 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/YEASTCHIP.DB/man/GENENAME.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@GENENAME} 2 | \alias{@ANNOBJPREFIX@GENENAME} 3 | \title{Map between Manufacturer IDs and Genes} 4 | \description{ 5 | @ANNOBJPREFIX@GENENAME is an R object that maps manufacturer 6 | identifiers to the corresponding gene name. 7 | } 8 | \details{ 9 | Each manufacturer identifier maps to a named vector containing the gene 10 | name. The vector name corresponds to the manufacturer identifier. If the gene 11 | name is unknown, the vector will contain an \code{NA}. 12 | 13 | Gene names currently include both the official (validated by a 14 | nomenclature committee) and preferred names (interim selected for 15 | display) for genes. Efforts are being made to differentiate the two 16 | by adding a name to the vector. 17 | 18 | Mappings were based on data provided by: @GENENAMESOURCE@ 19 | } 20 | 21 | \seealso{ 22 | \itemize{ 23 | \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of 24 | the \code{select()} interface. 25 | } 26 | } 27 | 28 | \examples{ 29 | ## select() interface: 30 | ## Objects in this package can be accessed using the select() interface 31 | ## from the AnnotationDbi package. See ?select for details. 32 | 33 | ## Bimap interface: 34 | x <- @ANNOBJPREFIX@GENENAME 35 | # Get the probe identifiers that are mapped to a gene name 36 | mapped_probes <- mappedkeys(x) 37 | # Convert to a list 38 | xx <- as.list(x[mapped_probes]) 39 | if(length(xx) > 0) { 40 | # Get the GENENAME for the first five probes 41 | xx[1:5] 42 | # Get the first one 43 | xx[[1]] 44 | } 45 | } 46 | \keyword{datasets} 47 | 48 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/BASEPKG.DB/man/BASE.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@.db0} 2 | \alias{@ANNOBJPREFIX@.db0} 3 | \alias{@ANNOBJPREFIX@} 4 | \title{Bioconductor annotation BASE package} 5 | \description{ 6 | Welcome to the @ANNOBJPREFIX@.db0 annotation Package. This is an 7 | organism specific package and is ONLY meant as a means for 8 | distributing the latest Annotation Databases needed by the sqlForge 9 | code inside of AnnotationDbi to produce normal Annotation Packages. 10 | 11 | Users are warned that the direct calling of the database inside this 12 | package could be a very bad idea depending on what you are planning to 13 | do. This is because the schema for the databases in this package 14 | COULD CHANGE AT ANY TIME. Because of this, no schemas are provided. 15 | 16 | For access to more consistent schemas, please use the sqlForge package 17 | to generate a normal chip or organism based annotation package, or 18 | else use one of these other annotation packages directly. 19 | } 20 | \examples{ 21 | \dontrun{ 22 | # You should never have to use this package for anything directly. 23 | # Its purpose is only to put the latest databases into a consistent 24 | # location so that the sqlForge code can build annotation packages from 25 | # them. All you should ever have to do is use BiocManager::install() 26 | # to obtain this package and then use the appropriate wrapper functions from 27 | # AnnotationDbi. Some examples Include: 28 | # makeHUMANCHIP_DB(), makeMOUSECHIP_DB(), makeRATCHIP_DB(), 29 | # makeFLYCHIP_DB(), makeYEASTCHIP_DB(), makeARABIDOPSISCHIP_DB() 30 | } 31 | } 32 | \keyword{datasets} 33 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/NCBIORG.DB/man/GENENAME.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@GENENAME} 2 | \alias{@ANNOBJPREFIX@GENENAME} 3 | \title{Map between Entrez Gene IDs and Genes} 4 | \description{ 5 | @ANNOBJPREFIX@GENENAME is an R object that maps entrez gene 6 | identifiers to the corresponding gene name. 7 | } 8 | 9 | \details{ 10 | Each entrez gene identifier maps to a named vector containing the gene 11 | name. The vector name corresponds to the entrez gene identifier. If the 12 | gene name is unknown, the vector will contain an \code{NA}. 13 | 14 | Gene names currently include both the official (validated by a 15 | nomenclature committee) and preferred names (interim selected for 16 | display) for genes. Efforts are being made to differentiate the two 17 | by adding a name to the vector. 18 | 19 | Mappings were based on data provided by: @GENENAMESOURCE@ 20 | } 21 | 22 | \seealso{ 23 | \itemize{ 24 | \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of 25 | the \code{select()} interface. 26 | } 27 | } 28 | 29 | \examples{ 30 | ## select() interface: 31 | ## Objects in this package can be accessed using the select() interface 32 | ## from the AnnotationDbi package. See ?select for details. 33 | 34 | ## Bimap interface: 35 | x <- @ANNOBJPREFIX@GENENAME 36 | # Get the gene names that are mapped to an entrez gene identifier 37 | mapped_genes <- mappedkeys(x) 38 | # Convert to a list 39 | xx <- as.list(x[mapped_genes]) 40 | if(length(xx) > 0) { 41 | # Get the GENE NAME for the first five genes 42 | xx[1:5] 43 | # Get the first one 44 | xx[[1]] 45 | } 46 | } 47 | \keyword{datasets} 48 | 49 | 50 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/ARABIDOPSISCHIP.DB/man/GENENAME.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@GENENAME} 2 | \alias{@ANNOBJPREFIX@GENENAME} 3 | \title{Map between Manufacturer IDs and Genes} 4 | \description{ 5 | @ANNOBJPREFIX@GENENAME is an R object that maps manufacturer 6 | identifiers to the corresponding gene name. 7 | } 8 | \details{ 9 | Each manufacturer identifier maps to a named vector containing the gene 10 | name. The vector name corresponds to the manufacturer identifier. If the gene 11 | name is unknown, the vector will contain an \code{NA}. 12 | 13 | Gene names currently include both the official (validated by a 14 | nomenclature committee) and preferred names (interim selected for 15 | display) for genes. Efforts are being made to differentiate the two 16 | by adding a name to the vector. 17 | 18 | Mappings were based on data provided by: @GENENAMESOURCE@ 19 | 20 | } 21 | 22 | \seealso{ 23 | \itemize{ 24 | \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of 25 | the \code{select()} interface. 26 | } 27 | } 28 | 29 | \examples{ 30 | ## select() interface: 31 | ## Objects in this package can be accessed using the select() interface 32 | ## from the AnnotationDbi package. See ?select for details. 33 | 34 | ## Bimap interface: 35 | x <- @ANNOBJPREFIX@GENENAME 36 | # Get the probe identifiers that are mapped to a gene name 37 | mapped_probes <- mappedkeys(x) 38 | # Convert to a list 39 | xx <- as.list(x[mapped_probes]) 40 | if(length(xx) > 0) { 41 | # Get the GENENAME for the first five probes 42 | xx[1:5] 43 | # Get the first one 44 | xx[[1]] 45 | } 46 | } 47 | \keyword{datasets} 48 | 49 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/COELICOLOR.DB/man/GENENAME.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@GENENAME} 2 | \alias{@ANNOBJPREFIX@GENENAME} 3 | \title{Map between Entrez Gene IDs and Genes} 4 | \description{ 5 | @ANNOBJPREFIX@GENENAME is an R object that maps entrez gene 6 | identifiers to the corresponding gene name. 7 | } 8 | \details{ 9 | Each entrez gene identifier maps to a named vector containing the gene 10 | name. The vector name corresponds to the entrez gene identifier. If the 11 | gene name is unknown, the vector will contain an \code{NA}. 12 | 13 | Gene names currently include both the official (validated by a 14 | nomenclature committee) and preferred names (interim selected for 15 | display) for genes. Efforts are being made to differentiate the two 16 | by adding a name to the vector. 17 | 18 | Mappings were based on data provided by: @GENENAMESOURCE@ 19 | 20 | } 21 | 22 | \seealso{ 23 | \itemize{ 24 | \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of 25 | the \code{select()} interface. 26 | } 27 | } 28 | 29 | \examples{ 30 | ## select() interface: 31 | ## Objects in this package can be accessed using the select() interface 32 | ## from the AnnotationDbi package. See ?select for details. 33 | 34 | ## Bimap interface: 35 | x <- @ANNOBJPREFIX@GENENAME 36 | # Get the gene names that are mapped to an entrez gene identifier 37 | mapped_genes <- mappedkeys(x) 38 | # Convert to a list 39 | xx <- as.list(x[mapped_genes]) 40 | if(length(xx) > 0) { 41 | # Get the GENE NAME for the first five genes 42 | xx[1:5] 43 | # Get the first one 44 | xx[[1]] 45 | } 46 | } 47 | \keyword{datasets} 48 | 49 | 50 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/NCBICHIP.DB/man/GENENAME.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@GENENAME} 2 | \alias{@ANNOBJPREFIX@GENENAME} 3 | \title{Map between Manufacturer IDs and Genes} 4 | \description{ 5 | @ANNOBJPREFIX@GENENAME is an R object that maps manufacturer 6 | identifiers to the corresponding gene name. 7 | } 8 | \details{ 9 | Each manufacturer identifier maps to a named vector containing the gene 10 | name. The vector name corresponds to the manufacturer identifier. If the gene 11 | name is unknown, the vector will contain an \code{NA}. 12 | 13 | Gene names currently include both the official (validated by a 14 | nomenclature committee) and preferred names (interim selected for 15 | display) for genes. Efforts are being made to differentiate the two 16 | by adding a name to the vector. 17 | 18 | Mappings were based on data provided by: @GENENAMESOURCE@ 19 | 20 | } 21 | 22 | \seealso{ 23 | \itemize{ 24 | \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of 25 | the \code{select()} interface. 26 | } 27 | } 28 | 29 | \examples{ 30 | ## select() interface: 31 | ## Objects in this package can be accessed using the select() interface 32 | ## from the AnnotationDbi package. See ?select for details. 33 | 34 | ## Bimap interface: 35 | x <- @ANNOBJPREFIX@GENENAME 36 | # Get the probe identifiers that are mapped to a gene name 37 | mapped_probes <- mappedkeys(x) 38 | # Convert to a list 39 | xx <- as.list(x[mapped_probes][1:300]) 40 | if(length(xx) > 0) { 41 | # Get the GENENAME for the first five probes 42 | xx[1:5] 43 | # Get the first one 44 | xx[[1]] 45 | } 46 | } 47 | \keyword{datasets} 48 | 49 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/NCBIORG.DB/man/MGI.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@MGI} 2 | \alias{@ANNOBJPREFIX@MGI} 3 | \alias{@ANNOBJPREFIX@MGI2EG} 4 | \title{Map MGI gene Acession numbers with Entrez Gene identifiers} 5 | \description{ 6 | @ANNOBJPREFIX@MGI is an R object that contains mappings between 7 | Entrez Gene identifiers and Jackson Laboratory MGI gene accession numbers. 8 | } 9 | \details{ 10 | This object is a simple mapping of Entrez Gene identifiers 11 | \url{https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene} to MGI 12 | gene Accession Numbers. 13 | 14 | Mappings were based on data provided by: @MGISOURCE@ 15 | } 16 | 17 | \seealso{ 18 | \itemize{ 19 | \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of 20 | the \code{select()} interface. 21 | } 22 | } 23 | 24 | \examples{ 25 | ## select() interface: 26 | ## Objects in this package can be accessed using the select() interface 27 | ## from the AnnotationDbi package. See ?select for details. 28 | 29 | ## Bimap interface: 30 | x <- @ANNOBJPREFIX@MGI 31 | # Get the entrez gene IDs that are mapped to an MGI ID 32 | mapped_genes <- mappedkeys(x) 33 | # Convert to a list 34 | xx <- as.list(x[mapped_genes]) 35 | if(length(xx) > 0) { 36 | # Get the MGI gene IDs for the first five genes 37 | xx[1:5] 38 | # Get the first one 39 | xx[[1]] 40 | } 41 | #For the reverse map MGI2EG: 42 | # Convert to a list 43 | xx <- as.list(@ANNOBJPREFIX@MGI2EG) 44 | if(length(xx) > 0){ 45 | # Gets the entrez gene IDs for the first five MGI IDs 46 | xx[1:5] 47 | # Get the first one 48 | xx[[1]] 49 | } 50 | } 51 | \keyword{datasets} 52 | 53 | 54 | 55 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/YEASTNCBI.DB/man/GENENAME.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@GENENAME} 2 | \alias{@ANNOBJPREFIX@GENENAME} 3 | \title{Map between Entrez Gene IDs and Genes} 4 | \description{ 5 | @ANNOBJPREFIX@GENENAME is an R object that maps entrez gene 6 | identifiers to the corresponding gene name. 7 | } 8 | \details{ 9 | Each entrez gene identifier maps to a named vector containing the gene 10 | name. The vector name corresponds to the entrez gene identifier. If the 11 | gene name is unknown, the vector will contain an \code{NA}. 12 | 13 | Gene names currently include both the official (validated by a 14 | nomenclature committee) and preferred names (interim selected for 15 | display) for genes. Efforts are being made to differentiate the two 16 | by adding a name to the vector. 17 | 18 | Mappings were based on data provided by: @GENENAMESOURCE@ 19 | 20 | } 21 | 22 | \seealso{ 23 | \itemize{ 24 | \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of 25 | the \code{select()} interface. 26 | } 27 | } 28 | 29 | \examples{ 30 | ## select() interface: 31 | ## Objects in this package can be accessed using the select() interface 32 | ## from the AnnotationDbi package. See ?select for details. 33 | 34 | ## Bimap interface: 35 | x <- @ANNOBJPREFIX@GENENAME 36 | # Get the gene names that are mapped to an entrez gene identifier 37 | mapped_genes <- mappedkeys(x) 38 | # Convert to a list 39 | xx <- as.list(x[mapped_genes]) 40 | if(length(xx) > 0) { 41 | # Get the GENE NAME for the first five genes 42 | xx[1:5] 43 | # Get the first one 44 | xx[[1]] 45 | } 46 | } 47 | \keyword{datasets} 48 | 49 | 50 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/ORGANISM.DB/man/GENENAME.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@GENENAME} 2 | \alias{@ANNOBJPREFIX@GENENAME} 3 | \title{Map between Entrez Gene IDs and Genes} 4 | \description{ 5 | @ANNOBJPREFIX@GENENAME is an R object that maps entrez gene 6 | identifiers to the corresponding gene name. 7 | } 8 | \details{ 9 | Each entrez gene identifier maps to a named vector containing the gene 10 | name. The vector name corresponds to the entrez gene identifier. If the 11 | gene name is unknown, the vector will contain an \code{NA}. 12 | 13 | Gene names currently include both the official (validated by a 14 | nomenclature committee) and preferred names (interim selected for 15 | display) for genes. Efforts are being made to differentiate the two 16 | by adding a name to the vector. 17 | 18 | Mappings were based on data provided by: @GENENAMESOURCE@ 19 | 20 | } 21 | 22 | \seealso{ 23 | \itemize{ 24 | \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of 25 | the \code{select()} interface. 26 | } 27 | } 28 | 29 | \examples{ 30 | ## select() interface: 31 | ## Objects in this package can be accessed using the select() interface 32 | ## from the AnnotationDbi package. See ?select for details. 33 | 34 | ## Bimap interface: 35 | x <- @ANNOBJPREFIX@GENENAME 36 | # Get the gene names that are mapped to an entrez gene identifier 37 | mapped_genes <- mappedkeys(x) 38 | # Convert to a list 39 | xx <- as.list(x[mapped_genes]) 40 | if(length(xx) > 0) { 41 | # Get the GENE NAME for the first five genes 42 | xx[1:5] 43 | # Get the first one 44 | xx[[1]] 45 | } 46 | } 47 | 48 | \keyword{datasets} 49 | 50 | 51 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/NCBICHIP.DB/man/MGI.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@MGI} 2 | \alias{@ANNOBJPREFIX@MGI} 3 | \alias{@ANNOBJPREFIX@MGI2PROBE} 4 | \title{Map MGI gene accession numbers with manufacturer identifiers} 5 | \description{ 6 | @ANNOBJPREFIX@MGI is an R object that contains mappings between 7 | manufacturer identifiers and Jackson Laboratory MGI gene accession numbers. 8 | } 9 | \details{ 10 | This object is a simple mapping of manufacturer identifiers to MGI 11 | gene Accession Numbers. 12 | 13 | Mappings were based on data provided by: @MGISOURCE@ 14 | } 15 | 16 | \seealso{ 17 | \itemize{ 18 | \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of 19 | the \code{select()} interface. 20 | } 21 | } 22 | 23 | \examples{ 24 | ## select() interface: 25 | ## Objects in this package can be accessed using the select() interface 26 | ## from the AnnotationDbi package. See ?select for details. 27 | 28 | ## Bimap interface: 29 | x <- @ANNOBJPREFIX@MGI 30 | # Get the manufacturer IDs that are mapped to an MGI ID 31 | mapped_genes <- mappedkeys(x) 32 | # Convert to a list 33 | xx <- as.list(x[mapped_genes][1:300]) 34 | if(length(xx) > 0) { 35 | # Get the MGI IDs for the first five genes 36 | xx[1:5] 37 | # Get the first one 38 | xx[[1]] 39 | } 40 | #For the reverse map MGI2EG: 41 | x <- @ANNOBJPREFIX@MGI2EG 42 | mapped_genes <- mappedkeys(x) 43 | # Convert to a list 44 | xx <- as.list(x[mapped_genes][1:300]) 45 | if(length(xx) > 0){ 46 | # Gets the manufacturer IDs for the first five MGI IDs 47 | xx[1:5] 48 | # Get the first one 49 | xx[[1]] 50 | } 51 | } 52 | \keyword{datasets} 53 | 54 | 55 | 56 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/ARABIDOPSIS.DB/man/SYMBOL.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@SYMBOL} 2 | \alias{@ANNOBJPREFIX@SYMBOL} 3 | \title{Map between TAIR Identifiers and Gene Symbols} 4 | \description{ 5 | @ANNOBJPREFIX@SYMBOL is an R object that provides mappings between 6 | TAIR identifiers and gene abbreviations. 7 | } 8 | \details{ 9 | Each TAIR identifier is mapped to an abbreviation for the 10 | corresponding gene. An \code{NA} is reported if there is no known 11 | abbreviation for a given gene. 12 | 13 | Symbols typically consist of 3 letters that define either a single 14 | gene (ABC) or multiple genes (ABC1, ABC2, ABC3). Gene symbols can be 15 | used as key words to query public databases such as Entrez Gene. 16 | 17 | Mappings were based on data provided by: @SYMBOLSOURCE@ 18 | 19 | } 20 | 21 | \references{ 22 | \url{https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene} 23 | } 24 | 25 | \seealso{ 26 | \itemize{ 27 | \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of 28 | the \code{select()} interface. 29 | } 30 | } 31 | 32 | \examples{ 33 | ## select() interface: 34 | ## Objects in this package can be accessed using the select() interface 35 | ## from the AnnotationDbi package. See ?select for details. 36 | 37 | ## Bimap interface: 38 | x <- @ANNOBJPREFIX@SYMBOL 39 | # Get the tair identifiers that are mapped to a gene symbol 40 | mapped_genes <- mappedkeys(x) 41 | # Convert to a list 42 | xx <- as.list(x[mapped_genes]) 43 | if(length(xx) > 0) { 44 | # Get the SYMBOL for the first five genes 45 | xx[1:5] 46 | # Get the first one 47 | xx[[1]] 48 | } 49 | } 50 | 51 | \keyword{datasets} 52 | 53 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/YEAST.DB/man/DESCRIPTION.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@DESCRIPTION} 2 | \alias{@ANNOBJPREFIX@DESCRIPTION} 3 | \title{An annotation data file that maps Open Reading Frame (ORF) 4 | identifiers to textural descriptions of the corresponding genes} 5 | \description{ 6 | @ANNOBJPREFIX@DESCRIPTION maps yeast ORF identifiers to descriptive information 7 | about genes corresponding to the ORF identifiers 8 | } 9 | \details{ 10 | This is an R object containing key and value pairs. Keys are 11 | ORF identifiers and values are the corresponding descriptions of genes. Values 12 | are vectors of length 1. Probe identifiers that can not be mapped to 13 | descriptive information are assigned a value NA. 14 | 15 | Annotation based on data provided by: @DESCRIPTIONSOURCE@ 16 | 17 | } 18 | 19 | \references{ 20 | \url{http://www.yeastgenome.org/DownloadContents.shtml} 21 | } 22 | 23 | \seealso{ 24 | \itemize{ 25 | \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of 26 | the \code{select()} interface. 27 | } 28 | } 29 | 30 | \examples{ 31 | ## select() interface: 32 | ## Objects in this package can be accessed using the select() interface 33 | ## from the AnnotationDbi package. See ?select for details. 34 | 35 | ## Bimap interface: 36 | x <- @ANNOBJPREFIX@DESCRIPTION 37 | # Get the probe identifiers that are mapped to gene descriptions 38 | mapped_probes <- mappedkeys(x) 39 | # Convert to a list 40 | xx <- as.list(x[mapped_probes]) 41 | if(length(xx) > 0) { 42 | # Get the gene descriptions for the first five probes 43 | xx[1:5] 44 | # For the first probe 45 | xx[[1]] 46 | } 47 | } 48 | \keyword{datasets} 49 | 50 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/PFAM.DB/man/SCOP2AC.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@SCOP2AC} 2 | \alias{@ANNOBJPREFIX@SCOP2AC} 3 | \title{Mappings from a SCOP ID to a PFAM Accession number} 4 | \description{ 5 | This is an R object that always contains mappings from a SCOP ID to a 6 | PFAM accession (AC) 7 | } 8 | \details{ 9 | The PFAM accession number has been attached to the SCOP IDs in this object. 10 | 11 | More Details: Structural Classification of Proteins 12 | (\url{http://scop.mrc-lmb.cam.ac.uk/scop/index.html}). Reference: 13 | Murzin A. G., Brenner S. E., Hubbard T., Chothia C. (1995). SCOP: a 14 | structural classification of proteins database for the investigation 15 | of sequences and structures. J. Mol. Biol. 247, 536-540 16 | } 17 | \references{\url{http://www.sanger.ac.uk/Software/Pfam/} and 18 | \url{ftp://ftp.sanger.ac.uk/pub/databases/Pfam/current_release/userman.txt} 19 | } 20 | 21 | \seealso{ 22 | \itemize{ 23 | \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of 24 | the \code{select()} interface. 25 | } 26 | } 27 | 28 | \examples{ 29 | ## select() interface: 30 | ## Objects in this package can be accessed using the select() interface 31 | ## from the AnnotationDbi package. See ?select for details. 32 | 33 | ## Bimap interface: 34 | #To map from SCOP to PFAM IDs: 35 | x <- @ANNOBJPREFIX@SCOP2AC 36 | # Get the SCOP identifiers that are mapped to a PFAM ID 37 | mapped_keys <- mappedkeys(x) 38 | # Convert to a list 39 | xx <- as.list(x[mapped_keys]) 40 | if(length(xx) > 0) { 41 | # Get the SCOP ID for the first five CAZYs 42 | xx[1:5] 43 | # Get the first one 44 | xx[[1]] 45 | } 46 | } 47 | \keyword{datasets} 48 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/NCBICHIP.DB/man/ALIAS2PROBE.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@ALIAS2PROBE} 2 | \alias{@ANNOBJPREFIX@ALIAS2PROBE} 3 | \title{Map between Common Gene Symbol Identifiers and Manufacturer Identifiers} 4 | \description{ 5 | @ANNOBJPREFIX@ALIAS is an R object that provides mappings between 6 | common gene symbol identifiers and manufacturer identifiers. 7 | } 8 | \details{ 9 | Each gene symbol is mapped to a named vector of manufacturer identifiers. The 10 | name represents the gene symbol and the vector contains all manufacturer 11 | identifiers that are found for that symbol. An \code{NA} is reported for any 12 | gene symbol that cannot be mapped to any manufacturer identifiers. 13 | 14 | This mapping includes ALL gene symbols including those which are already 15 | listed in the SYMBOL map. The SYMBOL map is meant to only list official gene 16 | symbols, while the ALIAS maps are meant to store all used symbols. 17 | 18 | Mappings were based on data provided by: @ALIAS2PROBESOURCE@ 19 | } 20 | 21 | \seealso{ 22 | \itemize{ 23 | \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of 24 | the \code{select()} interface. 25 | } 26 | } 27 | 28 | \examples{ 29 | ## select() interface: 30 | ## Objects in this package can be accessed using the select() interface 31 | ## from the AnnotationDbi package. See ?select for details. 32 | 33 | ## Bimap interface: 34 | # Convert the object to a list 35 | xx <- as.list(@ANNOBJPREFIX@ALIAS2PROBE) 36 | if(length(xx) > 0){ 37 | # Get the probe identifiers for the first two aliases 38 | xx[1:2] 39 | # Get the first one 40 | xx[[1]] 41 | } 42 | } 43 | 44 | \keyword{datasets} 45 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/YEASTCHIP.DB/man/DESCRIPTION.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@DESCRIPTION} 2 | \alias{@ANNOBJPREFIX@DESCRIPTION} 3 | \title{An annotation data file that maps Open Reading Frame (ORF) 4 | identifiers to textural descriptions of the corresponding genes} 5 | \description{ 6 | @ANNOBJPREFIX@DESCRIPTION maps yeast ORF identifiers to descriptive information 7 | about genes corresponding to the ORF identifiers 8 | } 9 | \details{ 10 | This is an R object containing key and value pairs. Keys are 11 | ORF identifiers and values are the corresponding descriptions of genes. Values 12 | are vectors of length 1. Probe identifiers that can not be mapped to 13 | descriptive information are assigned a value NA. 14 | 15 | Annotation based on data provided by: @DESCRIPTIONSOURCE@ 16 | 17 | } 18 | 19 | \references{ 20 | \url{http://www.yeastgenome.org/DownloadContents.shtml} 21 | } 22 | 23 | \seealso{ 24 | \itemize{ 25 | \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of 26 | the \code{select()} interface. 27 | } 28 | } 29 | 30 | \examples{ 31 | ## select() interface: 32 | ## Objects in this package can be accessed using the select() interface 33 | ## from the AnnotationDbi package. See ?select for details. 34 | 35 | ## Bimap interface: 36 | x <- @ANNOBJPREFIX@DESCRIPTION 37 | # Get the probe identifiers that are mapped to gene descriptions 38 | mapped_probes <- mappedkeys(x) 39 | # Convert to a list 40 | xx <- as.list(x[mapped_probes]) 41 | if(length(xx) > 0) { 42 | # Get the gene descriptions for the first five probes 43 | xx[1:5] 44 | # For the first probe 45 | xx[[1]] 46 | } 47 | } 48 | 49 | \keyword{datasets} 50 | 51 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/COELICOLOR.DB/man/ACCNUM.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@ACCNUM} 2 | \alias{@ANNOBJPREFIX@ACCNUM} 3 | \alias{@ANNOBJPREFIX@ACCNUM2EG} 4 | \title{Map Entrez Gene identifiers to GenBank Accession Numbers} 5 | \description{ 6 | @ANNOBJPREFIX@ACCNUM is an R object that contains mappings between 7 | Entrez Gene identifiers and GenBank accession numbers. 8 | } 9 | \details{ 10 | This object is a simple mapping of Entrez Gene identifiers 11 | \url{https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene} to all possible 12 | GenBank accession numbers. 13 | 14 | Mappings were based on data provided by: @ACCNUMSOURCE@ 15 | } 16 | 17 | \seealso{ 18 | \itemize{ 19 | \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of 20 | the \code{select()} interface. 21 | } 22 | } 23 | 24 | \examples{ 25 | ## select() interface: 26 | ## Objects in this package can be accessed using the select() interface 27 | ## from the AnnotationDbi package. See ?select for details. 28 | 29 | ## Bimap interface: 30 | x <- @ANNOBJPREFIX@ACCNUM 31 | # Get the entrez gene identifiers that are mapped to an ACCNUM 32 | mapped_genes <- mappedkeys(x) 33 | # Convert to a list 34 | xx <- as.list(x[mapped_genes]) 35 | if(length(xx) > 0) { 36 | # Get the ACCNUM for the first five genes 37 | xx[1:5] 38 | # Get the first one 39 | xx[[1]] 40 | } 41 | #For the reverse map ACCNUM2EG: 42 | # Convert to a list 43 | xx <- as.list(@ANNOBJPREFIX@ACCNUM2EG) 44 | if(length(xx) > 0){ 45 | # Gets the entrez gene identifiers for the first five Entrez Gene IDs 46 | xx[1:5] 47 | # Get the first one 48 | xx[[1]] 49 | } 50 | } 51 | \keyword{datasets} 52 | 53 | 54 | 55 | -------------------------------------------------------------------------------- /inst/AnnDbPkg-templates/NCBIORG.DB/man/FLYBASE.Rd: -------------------------------------------------------------------------------- 1 | \name{@ANNOBJPREFIX@FLYBASE} 2 | \alias{@ANNOBJPREFIX@FLYBASE} 3 | \alias{@ANNOBJPREFIX@FLYBASE2EG} 4 | \title{Map FlyBase acession numbers with Entrez Gene identifiers} 5 | \description{ 6 | @ANNOBJPREFIX@FLYBASE is an R object that contains mappings between 7 | Entrez Gene identifiers and FlyBase accession numbers. 8 | } 9 | \details{ 10 | This object is a simple mapping of Entrez Gene identifiers 11 | \url{https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene} to Flybase 12 | accession numbers. 13 | 14 | Mappings were based on data provided by: @FLYBASESOURCE@ 15 | } 16 | 17 | \seealso{ 18 | \itemize{ 19 | \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of 20 | the \code{select()} interface. 21 | } 22 | } 23 | 24 | \examples{ 25 | ## select() interface: 26 | ## Objects in this package can be accessed using the select() interface 27 | ## from the AnnotationDbi package. See ?select for details. 28 | 29 | ## Bimap interface: 30 | x <- @ANNOBJPREFIX@FLYBASE 31 | # Get the entrez gene identifiers that are mapped to a Flybase ID 32 | mapped_genes <- mappedkeys(x) 33 | # Convert to a list 34 | xx <- as.list(x[mapped_genes]) 35 | if(length(xx) > 0) { 36 | # Get the FlyBase IDs for the first five genes 37 | xx[1:5] 38 | # Get the first one 39 | xx[[1]] 40 | } 41 | #For the reverse map FLYBASE2EG: 42 | # Convert to a list 43 | xx <- as.list(@ANNOBJPREFIX@FLYBASE2EG) 44 | if(length(xx) > 0){ 45 | # Gets the entrez gene identifiers for the first five FlyBase IDs 46 | xx[1:5] 47 | # Get the first one 48 | xx[[1]] 49 | } 50 | } 51 | \keyword{datasets} 52 | 53 | 54 | 55 | --------------------------------------------------------------------------------