├── .gitignore ├── .travis.yml ├── DESCRIPTION ├── NAMESPACE ├── NEWS ├── R ├── LMC_interpretation.R ├── MeDeCom-package.R ├── MeDeComSet-class.R ├── RcppExports.R ├── allGlobals.R ├── contribution_interpretation.R ├── factorizations.R ├── frontend.R ├── gapStatisitics.R ├── markerSelection.R ├── matching.R ├── plotting.R ├── reference.R ├── simulation.R └── utilities.R ├── README ├── README.md ├── data ├── datalist ├── example.MeDeComSet.RData ├── example.cg.annotation.RData ├── example.dataset.RData └── small.example.RnBSet.RData ├── exec └── cluster.script.sge.R ├── inst └── unitTests │ └── test_general.R ├── man ├── AVAIL.REFS.Rd ├── MeDeCom-package.Rd ├── MeDeComSet-class.Rd ├── as.MeDeComSet.Rd ├── cluster.refbased.Rd ├── example.MeDeComSet.Rd ├── example.cg.annotation.Rd ├── example.dataset.Rd ├── factorize.alternate.Rd ├── factorize.regr.Rd ├── getLMCs-methods.Rd ├── getProportions-methods.Rd ├── getStatistics-methods.Rd ├── greedymatch.Rd ├── lmc.annotation.enrichment.Rd ├── lmc.annotation.plots.tables.Rd ├── lmc.go.enrichment.Rd ├── lmc.go.plots.tables.Rd ├── lmc.lola.enrichment.Rd ├── lmc.lola.plots.tables.Rd ├── load.lola.for.medecom.Rd ├── locus_plot.Rd ├── matchLMCs.Rd ├── plotLMC.reference.Rd ├── plotLMCs.Rd ├── plotParameters.Rd ├── plotProportions.Rd ├── run.refbased.Rd ├── run.trait.association.Rd ├── run.trait.association.single.Rd └── runMeDeCom.Rd ├── src ├── HCLasso.cpp ├── Makevars ├── Makevars.win ├── QuadHC.cpp ├── RProjSplxBox.cpp ├── RQuadSimplex.cpp ├── RQuadSimplexBox.cpp ├── RcppExports.cpp ├── cppTAfact.cpp └── dynblas.h ├── tests └── runTests.R └── vignettes ├── MeDeCom.Rmd ├── MeDeCom.html ├── MeDeCom.md ├── MeDeCom_files └── MathJax.js └── figure ├── unnamed-chunk-10-1.png ├── unnamed-chunk-11-1.png ├── unnamed-chunk-12-1.png ├── unnamed-chunk-13-1.png ├── unnamed-chunk-14-1.png ├── unnamed-chunk-17-1.png ├── unnamed-chunk-18-1.png ├── unnamed-chunk-19-1.png ├── unnamed-chunk-20-1.png ├── unnamed-chunk-22-1.png ├── unnamed-chunk-7-1.png └── unnamed-chunk-8-1.png /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompEpigen/MeDeCom/HEAD/.gitignore -------------------------------------------------------------------------------- /.travis.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompEpigen/MeDeCom/HEAD/.travis.yml -------------------------------------------------------------------------------- /DESCRIPTION: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompEpigen/MeDeCom/HEAD/DESCRIPTION -------------------------------------------------------------------------------- /NAMESPACE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompEpigen/MeDeCom/HEAD/NAMESPACE -------------------------------------------------------------------------------- /NEWS: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompEpigen/MeDeCom/HEAD/NEWS -------------------------------------------------------------------------------- /R/LMC_interpretation.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompEpigen/MeDeCom/HEAD/R/LMC_interpretation.R -------------------------------------------------------------------------------- /R/MeDeCom-package.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompEpigen/MeDeCom/HEAD/R/MeDeCom-package.R -------------------------------------------------------------------------------- /R/MeDeComSet-class.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompEpigen/MeDeCom/HEAD/R/MeDeComSet-class.R -------------------------------------------------------------------------------- /R/RcppExports.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompEpigen/MeDeCom/HEAD/R/RcppExports.R -------------------------------------------------------------------------------- /R/allGlobals.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompEpigen/MeDeCom/HEAD/R/allGlobals.R -------------------------------------------------------------------------------- /R/contribution_interpretation.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompEpigen/MeDeCom/HEAD/R/contribution_interpretation.R -------------------------------------------------------------------------------- /R/factorizations.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompEpigen/MeDeCom/HEAD/R/factorizations.R -------------------------------------------------------------------------------- /R/frontend.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompEpigen/MeDeCom/HEAD/R/frontend.R -------------------------------------------------------------------------------- /R/gapStatisitics.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompEpigen/MeDeCom/HEAD/R/gapStatisitics.R -------------------------------------------------------------------------------- /R/markerSelection.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompEpigen/MeDeCom/HEAD/R/markerSelection.R -------------------------------------------------------------------------------- /R/matching.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompEpigen/MeDeCom/HEAD/R/matching.R -------------------------------------------------------------------------------- /R/plotting.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompEpigen/MeDeCom/HEAD/R/plotting.R -------------------------------------------------------------------------------- /R/reference.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompEpigen/MeDeCom/HEAD/R/reference.R -------------------------------------------------------------------------------- /R/simulation.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompEpigen/MeDeCom/HEAD/R/simulation.R -------------------------------------------------------------------------------- /R/utilities.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompEpigen/MeDeCom/HEAD/R/utilities.R -------------------------------------------------------------------------------- /README: -------------------------------------------------------------------------------- 1 | MeDeCom -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompEpigen/MeDeCom/HEAD/README.md -------------------------------------------------------------------------------- /data/datalist: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompEpigen/MeDeCom/HEAD/data/datalist -------------------------------------------------------------------------------- /data/example.MeDeComSet.RData: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompEpigen/MeDeCom/HEAD/data/example.MeDeComSet.RData -------------------------------------------------------------------------------- /data/example.cg.annotation.RData: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompEpigen/MeDeCom/HEAD/data/example.cg.annotation.RData -------------------------------------------------------------------------------- /data/example.dataset.RData: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompEpigen/MeDeCom/HEAD/data/example.dataset.RData -------------------------------------------------------------------------------- /data/small.example.RnBSet.RData: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompEpigen/MeDeCom/HEAD/data/small.example.RnBSet.RData -------------------------------------------------------------------------------- /exec/cluster.script.sge.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompEpigen/MeDeCom/HEAD/exec/cluster.script.sge.R -------------------------------------------------------------------------------- /inst/unitTests/test_general.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompEpigen/MeDeCom/HEAD/inst/unitTests/test_general.R -------------------------------------------------------------------------------- /man/AVAIL.REFS.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompEpigen/MeDeCom/HEAD/man/AVAIL.REFS.Rd -------------------------------------------------------------------------------- /man/MeDeCom-package.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompEpigen/MeDeCom/HEAD/man/MeDeCom-package.Rd -------------------------------------------------------------------------------- /man/MeDeComSet-class.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompEpigen/MeDeCom/HEAD/man/MeDeComSet-class.Rd -------------------------------------------------------------------------------- /man/as.MeDeComSet.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompEpigen/MeDeCom/HEAD/man/as.MeDeComSet.Rd -------------------------------------------------------------------------------- /man/cluster.refbased.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompEpigen/MeDeCom/HEAD/man/cluster.refbased.Rd -------------------------------------------------------------------------------- /man/example.MeDeComSet.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompEpigen/MeDeCom/HEAD/man/example.MeDeComSet.Rd -------------------------------------------------------------------------------- /man/example.cg.annotation.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompEpigen/MeDeCom/HEAD/man/example.cg.annotation.Rd -------------------------------------------------------------------------------- /man/example.dataset.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompEpigen/MeDeCom/HEAD/man/example.dataset.Rd -------------------------------------------------------------------------------- /man/factorize.alternate.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompEpigen/MeDeCom/HEAD/man/factorize.alternate.Rd -------------------------------------------------------------------------------- /man/factorize.regr.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompEpigen/MeDeCom/HEAD/man/factorize.regr.Rd -------------------------------------------------------------------------------- /man/getLMCs-methods.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompEpigen/MeDeCom/HEAD/man/getLMCs-methods.Rd -------------------------------------------------------------------------------- /man/getProportions-methods.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompEpigen/MeDeCom/HEAD/man/getProportions-methods.Rd -------------------------------------------------------------------------------- /man/getStatistics-methods.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompEpigen/MeDeCom/HEAD/man/getStatistics-methods.Rd -------------------------------------------------------------------------------- /man/greedymatch.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompEpigen/MeDeCom/HEAD/man/greedymatch.Rd -------------------------------------------------------------------------------- /man/lmc.annotation.enrichment.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompEpigen/MeDeCom/HEAD/man/lmc.annotation.enrichment.Rd -------------------------------------------------------------------------------- /man/lmc.annotation.plots.tables.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompEpigen/MeDeCom/HEAD/man/lmc.annotation.plots.tables.Rd -------------------------------------------------------------------------------- /man/lmc.go.enrichment.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompEpigen/MeDeCom/HEAD/man/lmc.go.enrichment.Rd -------------------------------------------------------------------------------- /man/lmc.go.plots.tables.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompEpigen/MeDeCom/HEAD/man/lmc.go.plots.tables.Rd -------------------------------------------------------------------------------- /man/lmc.lola.enrichment.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompEpigen/MeDeCom/HEAD/man/lmc.lola.enrichment.Rd -------------------------------------------------------------------------------- /man/lmc.lola.plots.tables.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompEpigen/MeDeCom/HEAD/man/lmc.lola.plots.tables.Rd -------------------------------------------------------------------------------- /man/load.lola.for.medecom.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompEpigen/MeDeCom/HEAD/man/load.lola.for.medecom.Rd -------------------------------------------------------------------------------- /man/locus_plot.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompEpigen/MeDeCom/HEAD/man/locus_plot.Rd -------------------------------------------------------------------------------- /man/matchLMCs.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompEpigen/MeDeCom/HEAD/man/matchLMCs.Rd -------------------------------------------------------------------------------- /man/plotLMC.reference.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompEpigen/MeDeCom/HEAD/man/plotLMC.reference.Rd -------------------------------------------------------------------------------- /man/plotLMCs.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompEpigen/MeDeCom/HEAD/man/plotLMCs.Rd -------------------------------------------------------------------------------- /man/plotParameters.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompEpigen/MeDeCom/HEAD/man/plotParameters.Rd -------------------------------------------------------------------------------- /man/plotProportions.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompEpigen/MeDeCom/HEAD/man/plotProportions.Rd -------------------------------------------------------------------------------- /man/run.refbased.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompEpigen/MeDeCom/HEAD/man/run.refbased.Rd -------------------------------------------------------------------------------- /man/run.trait.association.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompEpigen/MeDeCom/HEAD/man/run.trait.association.Rd -------------------------------------------------------------------------------- /man/run.trait.association.single.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompEpigen/MeDeCom/HEAD/man/run.trait.association.single.Rd -------------------------------------------------------------------------------- /man/runMeDeCom.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompEpigen/MeDeCom/HEAD/man/runMeDeCom.Rd -------------------------------------------------------------------------------- /src/HCLasso.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompEpigen/MeDeCom/HEAD/src/HCLasso.cpp -------------------------------------------------------------------------------- /src/Makevars: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompEpigen/MeDeCom/HEAD/src/Makevars -------------------------------------------------------------------------------- /src/Makevars.win: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompEpigen/MeDeCom/HEAD/src/Makevars.win -------------------------------------------------------------------------------- /src/QuadHC.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompEpigen/MeDeCom/HEAD/src/QuadHC.cpp -------------------------------------------------------------------------------- /src/RProjSplxBox.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompEpigen/MeDeCom/HEAD/src/RProjSplxBox.cpp -------------------------------------------------------------------------------- /src/RQuadSimplex.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompEpigen/MeDeCom/HEAD/src/RQuadSimplex.cpp -------------------------------------------------------------------------------- /src/RQuadSimplexBox.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompEpigen/MeDeCom/HEAD/src/RQuadSimplexBox.cpp -------------------------------------------------------------------------------- /src/RcppExports.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompEpigen/MeDeCom/HEAD/src/RcppExports.cpp -------------------------------------------------------------------------------- /src/cppTAfact.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompEpigen/MeDeCom/HEAD/src/cppTAfact.cpp -------------------------------------------------------------------------------- /src/dynblas.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompEpigen/MeDeCom/HEAD/src/dynblas.h -------------------------------------------------------------------------------- /tests/runTests.R: -------------------------------------------------------------------------------- 1 | BiocGenerics:::testPackage("MeDeCom") -------------------------------------------------------------------------------- /vignettes/MeDeCom.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompEpigen/MeDeCom/HEAD/vignettes/MeDeCom.Rmd -------------------------------------------------------------------------------- /vignettes/MeDeCom.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompEpigen/MeDeCom/HEAD/vignettes/MeDeCom.html -------------------------------------------------------------------------------- /vignettes/MeDeCom.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompEpigen/MeDeCom/HEAD/vignettes/MeDeCom.md -------------------------------------------------------------------------------- /vignettes/MeDeCom_files/MathJax.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompEpigen/MeDeCom/HEAD/vignettes/MeDeCom_files/MathJax.js -------------------------------------------------------------------------------- /vignettes/figure/unnamed-chunk-10-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompEpigen/MeDeCom/HEAD/vignettes/figure/unnamed-chunk-10-1.png -------------------------------------------------------------------------------- /vignettes/figure/unnamed-chunk-11-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompEpigen/MeDeCom/HEAD/vignettes/figure/unnamed-chunk-11-1.png -------------------------------------------------------------------------------- /vignettes/figure/unnamed-chunk-12-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompEpigen/MeDeCom/HEAD/vignettes/figure/unnamed-chunk-12-1.png -------------------------------------------------------------------------------- /vignettes/figure/unnamed-chunk-13-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompEpigen/MeDeCom/HEAD/vignettes/figure/unnamed-chunk-13-1.png -------------------------------------------------------------------------------- /vignettes/figure/unnamed-chunk-14-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompEpigen/MeDeCom/HEAD/vignettes/figure/unnamed-chunk-14-1.png -------------------------------------------------------------------------------- /vignettes/figure/unnamed-chunk-17-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompEpigen/MeDeCom/HEAD/vignettes/figure/unnamed-chunk-17-1.png -------------------------------------------------------------------------------- /vignettes/figure/unnamed-chunk-18-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompEpigen/MeDeCom/HEAD/vignettes/figure/unnamed-chunk-18-1.png -------------------------------------------------------------------------------- /vignettes/figure/unnamed-chunk-19-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompEpigen/MeDeCom/HEAD/vignettes/figure/unnamed-chunk-19-1.png -------------------------------------------------------------------------------- /vignettes/figure/unnamed-chunk-20-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompEpigen/MeDeCom/HEAD/vignettes/figure/unnamed-chunk-20-1.png -------------------------------------------------------------------------------- /vignettes/figure/unnamed-chunk-22-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompEpigen/MeDeCom/HEAD/vignettes/figure/unnamed-chunk-22-1.png -------------------------------------------------------------------------------- /vignettes/figure/unnamed-chunk-7-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompEpigen/MeDeCom/HEAD/vignettes/figure/unnamed-chunk-7-1.png -------------------------------------------------------------------------------- /vignettes/figure/unnamed-chunk-8-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompEpigen/MeDeCom/HEAD/vignettes/figure/unnamed-chunk-8-1.png --------------------------------------------------------------------------------