├── .Rbuildignore ├── .gitignore ├── .travis.yml ├── DESCRIPTION ├── NAMESPACE ├── NEWS.md ├── R ├── CreatePathwayCollection.R ├── accessClass_OmicsPath.R ├── accessClass_OmicsPathData.R ├── accessClass_OmicsRegCateg.R ├── accessClass_OmicsSurv.R ├── accessClass_pathwayCollection.R ├── accessClass_pathwayCollection_which.R ├── accessClass_pcOut.R ├── accessClass_pcOutpVals.R ├── aesPC_calculate_AESPCA.R ├── aesPC_calculate_LARS.R ├── aesPC_extract_OmicsPath_PCs.R ├── aesPC_permtest_CoxPH.R ├── aesPC_permtest_GLM.R ├── aesPC_permtest_LM.R ├── aesPC_unknown_matrixNorm.R ├── aesPC_wrapper.R ├── createClass_OmicsCateg.R ├── createClass_OmicsPath.R ├── createClass_OmicsReg.R ├── createClass_OmicsSurv.R ├── createClass_validOmics.R ├── createOmics_All.R ├── createOmics_CheckAssay.R ├── createOmics_CheckPathwayCollection.R ├── createOmics_CheckSampleIDs.R ├── createOmics_JoinPhenoAssay.R ├── createOmics_TrimPathwayCollection.R ├── createOmics_Wrapper.R ├── data_colonSubset.R ├── data_genesetSubset.R ├── data_wikipathways.R ├── data_wikipathways_symbols.R ├── pathwayPCA.R ├── printClass_Omics_All.R ├── printClass_pathwayCollection.R ├── superPC_model_CoxPH.R ├── superPC_model_GLM.R ├── superPC_model_LS.R ├── superPC_model_tStats.R ├── superPC_model_train.R ├── superPC_modifiedSVD.R ├── superPC_optimWeibullParams.R ├── superPC_optimWeibull_pValues.R ├── superPC_pathway_tControl.R ├── superPC_pathway_tScores.R ├── superPC_pathway_tValues.R ├── superPC_permuteSamples.R ├── superPC_wrapper.R ├── utils_Contains.R ├── utils_adjust_and_sort_pValues.R ├── utils_load_test_data_onto_PCs.R ├── utils_multtest_pvalues.R ├── utils_read_gmt.R ├── utils_stdExpr_2_tidyAssay.R ├── utils_transpose_assay.R └── utils_write_gmt.R ├── README.md ├── _pkgdown.yaml ├── data ├── colonSurv_df.rda ├── colon_pathwayCollection.rda ├── wikipwsHS_Entrez_pathwayCollection.rda └── wikipwsHS_Symbol_pathwayCollection.rda ├── docs ├── 404.html ├── articles │ ├── Introduction_to_pathwayPCA.html │ ├── Introduction_to_pathwayPCA_files │ │ └── figure-html │ │ │ ├── NFKB1SurvPlot-1.png │ │ │ ├── NFKB1plot-1.png │ │ │ ├── graphLoads-1.png │ │ │ ├── heatmapWP195-1.png │ │ │ ├── pathway_bar_plots-1.png │ │ │ ├── plotKidneyGroupedSurv-1.png │ │ │ ├── unnamed-chunk-1-1.png │ │ │ └── wp195PCs-1.png │ ├── Supplement1-Quickstart_Guide.html │ ├── Supplement1-Quickstart_Guide_files │ │ └── figure-html │ │ │ └── surv_spr_pval_plot-1.png │ ├── Supplement2-Importing_Data.html │ ├── Supplement3-Create_Omics_Objects.html │ ├── Supplement4-Methods_Walkthrough.html │ ├── Supplement5-Analyse_Results.html │ ├── Supplement5-Analyse_Results_files │ │ └── figure-html │ │ │ ├── bar_plots-1.png │ │ │ ├── pathway177_correlations_bar_chart-1.png │ │ │ ├── pathway177_loadings_bar_chart-1.png │ │ │ ├── pathway491_correlations_bar_chart-1.png │ │ │ ├── pathway491_loadings_bar_chart-1.png │ │ │ ├── surv_aes_pval_plot-1.png │ │ │ ├── unnamed-chunk-1-1.png │ │ │ └── unnamed-chunk-5-1.png │ ├── circlePlot.PNG │ ├── example_assay_data.PNG │ ├── example_pInfo_data.PNG │ └── index.html ├── authors.html ├── docsearch.css ├── docsearch.js ├── docsearch.json ├── favicon.ico ├── index.html ├── jquery.sticky-kit.min.js ├── link.svg ├── news │ └── index.html ├── pkgdown.css ├── pkgdown.js ├── pkgdown.yml ├── reference │ ├── AESPCA_pVals.html │ ├── CheckAssay.html │ ├── CheckPwyColl.html │ ├── CheckSampleIDs.html │ ├── Contains.html │ ├── ControlFDR.html │ ├── CreateOmics.html │ ├── CreateOmicsPathway.html │ ├── CreatePathwayCollection.html │ ├── ExtractAESPCs.html │ ├── GumbelMixpValues.html │ ├── IntersectOmicsPwyCollct.html │ ├── JoinPhenoAssay.html │ ├── LoadOntoPCs.html │ ├── OmicsCateg-class.html │ ├── OmicsPathway-class.html │ ├── OmicsReg-class.html │ ├── OmicsSurv-class.html │ ├── OptimGumbelMixParams.html │ ├── PathwaytValues.html │ ├── PermTestCateg.html │ ├── PermTestReg.html │ ├── PermTestSurv.html │ ├── SE2Tidy.html │ ├── SubsetPathwayCollection.html │ ├── SubsetPathwayData.html │ ├── TabulatepValues.html │ ├── TransposeAssay.html │ ├── ValidOmicsSurv.html │ ├── WhichPathways.html │ ├── aespca.html │ ├── colonSurv_df.html │ ├── colon_pathwayCollection.html │ ├── coxTrain_fun.html │ ├── getPathPCLs.html │ ├── getPathpVals.html │ ├── get_set_OmicsPathway.html │ ├── get_set_OmicsRegCateg.html │ ├── get_set_OmicsSurv.html │ ├── glmTrain_fun.html │ ├── index.html │ ├── lars.lsa.html │ ├── mysvd.html │ ├── normalize.html │ ├── olsTrain_fun.html │ ├── pathwayPCA-package.html │ ├── pathway_tControl.html │ ├── pathway_tScores.html │ ├── permuteSamps.html │ ├── print.pathwayCollection.html │ ├── read_gmt.html │ ├── show-OmicsPathway-method.html │ ├── superPCA_pVals.html │ ├── superpc.st.html │ ├── superpc.train.html │ ├── wikipwsHS_Entrez_pathwayCollection.html │ ├── wikipwsHS_Symbol_pathwayCollection.html │ └── write_gmt.html └── sitemap.xml ├── inst ├── extdata │ ├── c2.cp.v6.0.symbols.gmt │ ├── ex_assay_subset.csv │ ├── ex_pInfo_subset.csv │ ├── wikipathways_human.gmt │ └── wikipathways_human_symbol.gmt └── scripts │ ├── convert_EntrezID_to_HGNC_Ensembl.R │ ├── create_airway_example.R │ ├── generate_ex_subset.R │ ├── import_AP_gmt_20180601.R │ ├── issue_65_20220222.R │ └── multi_pathway_overlap_fishers.R ├── man ├── AESPCA_pVals.Rd ├── CheckAssay.Rd ├── CheckPwyColl.Rd ├── CheckSampleIDs.Rd ├── Contains.Rd ├── ControlFDR.Rd ├── CreateOmics.Rd ├── CreateOmicsPathway.Rd ├── CreatePathwayCollection.Rd ├── ExtractAESPCs.Rd ├── GumbelMixpValues.Rd ├── IntersectOmicsPwyCollct.Rd ├── JoinPhenoAssay.Rd ├── LoadOntoPCs.Rd ├── OmicsCateg-class.Rd ├── OmicsPathway-class.Rd ├── OmicsReg-class.Rd ├── OmicsSurv-class.Rd ├── OptimGumbelMixParams.Rd ├── PathwaytValues.Rd ├── PermTestCateg.Rd ├── PermTestReg.Rd ├── PermTestSurv.Rd ├── SE2Tidy.Rd ├── SubsetPathwayCollection.Rd ├── SubsetPathwayData.Rd ├── SuperPCA_pVals.Rd ├── TabulatepValues.Rd ├── TransposeAssay.Rd ├── ValidOmicsSurv.Rd ├── WhichPathways.Rd ├── aespca.Rd ├── colonSurv_df.Rd ├── colon_pathwayCollection.Rd ├── coxTrain_fun.Rd ├── getPathPCLs.Rd ├── getPathpVals.Rd ├── get_set_OmicsPathway.Rd ├── get_set_OmicsRegCateg.Rd ├── get_set_OmicsSurv.Rd ├── glmTrain_fun.Rd ├── lars.lsa.Rd ├── mysvd.Rd ├── normalize.Rd ├── olsTrain_fun.Rd ├── pathwayPCA-package.Rd ├── pathway_tControl.Rd ├── pathway_tScores.Rd ├── permuteSamps.Rd ├── print.pathwayCollection.Rd ├── read_gmt.Rd ├── show-OmicsPathway-method.Rd ├── superpc.st.Rd ├── superpc.train.Rd ├── wikipwsHS_Entrez_pathwayCollection.Rd ├── wikipwsHS_Symbol_pathwayCollection.Rd └── write_gmt.Rd ├── tests ├── testthat.R └── testthat │ ├── test_AESPCA_pVals.R │ ├── test_Contains.R │ ├── test_CreateOmicsWrapper.R │ ├── test_CreatePathwayCollection.R │ ├── test_LoadOntoPCs.R │ ├── test_SE2Tidy.R │ ├── test_SubsetPathwayData.R │ ├── test_SuperPCA_pVals.R │ ├── test_WhichPathways.R │ ├── test_getPathPCLs.R │ ├── test_getPathpVals.R │ ├── test_read_gmt.R │ └── test_write_gmt.R └── vignettes ├── Introduction_to_pathwayPCA.Rmd ├── Supplement1-Quickstart_Guide.Rmd ├── Supplement2-Importing_Data.Rmd ├── Supplement3-Create_Omics_Objects.Rmd ├── Supplement4-Methods_Walkthrough.Rmd ├── Supplement5-Analyse_Results.Rmd ├── circlePlot.PNG ├── circlePlotData.RDS ├── example_assay_data.PNG └── example_pInfo_data.PNG /.Rbuildignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/.Rbuildignore -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/.gitignore -------------------------------------------------------------------------------- /.travis.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/.travis.yml -------------------------------------------------------------------------------- /DESCRIPTION: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/DESCRIPTION -------------------------------------------------------------------------------- /NAMESPACE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/NAMESPACE -------------------------------------------------------------------------------- /NEWS.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/NEWS.md -------------------------------------------------------------------------------- /R/CreatePathwayCollection.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/R/CreatePathwayCollection.R -------------------------------------------------------------------------------- /R/accessClass_OmicsPath.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/R/accessClass_OmicsPath.R -------------------------------------------------------------------------------- /R/accessClass_OmicsPathData.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/R/accessClass_OmicsPathData.R -------------------------------------------------------------------------------- /R/accessClass_OmicsRegCateg.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/R/accessClass_OmicsRegCateg.R -------------------------------------------------------------------------------- /R/accessClass_OmicsSurv.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/R/accessClass_OmicsSurv.R -------------------------------------------------------------------------------- /R/accessClass_pathwayCollection.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/R/accessClass_pathwayCollection.R -------------------------------------------------------------------------------- /R/accessClass_pathwayCollection_which.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/R/accessClass_pathwayCollection_which.R -------------------------------------------------------------------------------- /R/accessClass_pcOut.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/R/accessClass_pcOut.R -------------------------------------------------------------------------------- /R/accessClass_pcOutpVals.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/R/accessClass_pcOutpVals.R -------------------------------------------------------------------------------- /R/aesPC_calculate_AESPCA.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/R/aesPC_calculate_AESPCA.R -------------------------------------------------------------------------------- /R/aesPC_calculate_LARS.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/R/aesPC_calculate_LARS.R -------------------------------------------------------------------------------- /R/aesPC_extract_OmicsPath_PCs.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/R/aesPC_extract_OmicsPath_PCs.R -------------------------------------------------------------------------------- /R/aesPC_permtest_CoxPH.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/R/aesPC_permtest_CoxPH.R -------------------------------------------------------------------------------- /R/aesPC_permtest_GLM.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/R/aesPC_permtest_GLM.R -------------------------------------------------------------------------------- /R/aesPC_permtest_LM.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/R/aesPC_permtest_LM.R -------------------------------------------------------------------------------- /R/aesPC_unknown_matrixNorm.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/R/aesPC_unknown_matrixNorm.R -------------------------------------------------------------------------------- /R/aesPC_wrapper.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/R/aesPC_wrapper.R -------------------------------------------------------------------------------- /R/createClass_OmicsCateg.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/R/createClass_OmicsCateg.R -------------------------------------------------------------------------------- /R/createClass_OmicsPath.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/R/createClass_OmicsPath.R -------------------------------------------------------------------------------- /R/createClass_OmicsReg.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/R/createClass_OmicsReg.R -------------------------------------------------------------------------------- /R/createClass_OmicsSurv.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/R/createClass_OmicsSurv.R -------------------------------------------------------------------------------- /R/createClass_validOmics.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/R/createClass_validOmics.R -------------------------------------------------------------------------------- /R/createOmics_All.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/R/createOmics_All.R -------------------------------------------------------------------------------- /R/createOmics_CheckAssay.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/R/createOmics_CheckAssay.R -------------------------------------------------------------------------------- /R/createOmics_CheckPathwayCollection.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/R/createOmics_CheckPathwayCollection.R -------------------------------------------------------------------------------- /R/createOmics_CheckSampleIDs.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/R/createOmics_CheckSampleIDs.R -------------------------------------------------------------------------------- /R/createOmics_JoinPhenoAssay.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/R/createOmics_JoinPhenoAssay.R -------------------------------------------------------------------------------- /R/createOmics_TrimPathwayCollection.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/R/createOmics_TrimPathwayCollection.R -------------------------------------------------------------------------------- /R/createOmics_Wrapper.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/R/createOmics_Wrapper.R -------------------------------------------------------------------------------- /R/data_colonSubset.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/R/data_colonSubset.R -------------------------------------------------------------------------------- /R/data_genesetSubset.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/R/data_genesetSubset.R -------------------------------------------------------------------------------- /R/data_wikipathways.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/R/data_wikipathways.R -------------------------------------------------------------------------------- /R/data_wikipathways_symbols.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/R/data_wikipathways_symbols.R -------------------------------------------------------------------------------- /R/pathwayPCA.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/R/pathwayPCA.R -------------------------------------------------------------------------------- /R/printClass_Omics_All.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/R/printClass_Omics_All.R -------------------------------------------------------------------------------- /R/printClass_pathwayCollection.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/R/printClass_pathwayCollection.R -------------------------------------------------------------------------------- /R/superPC_model_CoxPH.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/R/superPC_model_CoxPH.R -------------------------------------------------------------------------------- /R/superPC_model_GLM.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/R/superPC_model_GLM.R -------------------------------------------------------------------------------- /R/superPC_model_LS.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/R/superPC_model_LS.R -------------------------------------------------------------------------------- /R/superPC_model_tStats.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/R/superPC_model_tStats.R -------------------------------------------------------------------------------- /R/superPC_model_train.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/R/superPC_model_train.R -------------------------------------------------------------------------------- /R/superPC_modifiedSVD.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/R/superPC_modifiedSVD.R -------------------------------------------------------------------------------- /R/superPC_optimWeibullParams.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/R/superPC_optimWeibullParams.R -------------------------------------------------------------------------------- /R/superPC_optimWeibull_pValues.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/R/superPC_optimWeibull_pValues.R -------------------------------------------------------------------------------- /R/superPC_pathway_tControl.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/R/superPC_pathway_tControl.R -------------------------------------------------------------------------------- /R/superPC_pathway_tScores.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/R/superPC_pathway_tScores.R -------------------------------------------------------------------------------- /R/superPC_pathway_tValues.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/R/superPC_pathway_tValues.R -------------------------------------------------------------------------------- /R/superPC_permuteSamples.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/R/superPC_permuteSamples.R -------------------------------------------------------------------------------- /R/superPC_wrapper.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/R/superPC_wrapper.R -------------------------------------------------------------------------------- /R/utils_Contains.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/R/utils_Contains.R -------------------------------------------------------------------------------- /R/utils_adjust_and_sort_pValues.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/R/utils_adjust_and_sort_pValues.R -------------------------------------------------------------------------------- /R/utils_load_test_data_onto_PCs.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/R/utils_load_test_data_onto_PCs.R -------------------------------------------------------------------------------- /R/utils_multtest_pvalues.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/R/utils_multtest_pvalues.R -------------------------------------------------------------------------------- /R/utils_read_gmt.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/R/utils_read_gmt.R -------------------------------------------------------------------------------- /R/utils_stdExpr_2_tidyAssay.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/R/utils_stdExpr_2_tidyAssay.R -------------------------------------------------------------------------------- /R/utils_transpose_assay.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/R/utils_transpose_assay.R -------------------------------------------------------------------------------- /R/utils_write_gmt.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/R/utils_write_gmt.R -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/README.md -------------------------------------------------------------------------------- /_pkgdown.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/_pkgdown.yaml -------------------------------------------------------------------------------- /data/colonSurv_df.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/data/colonSurv_df.rda -------------------------------------------------------------------------------- /data/colon_pathwayCollection.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/data/colon_pathwayCollection.rda -------------------------------------------------------------------------------- /data/wikipwsHS_Entrez_pathwayCollection.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/data/wikipwsHS_Entrez_pathwayCollection.rda -------------------------------------------------------------------------------- /data/wikipwsHS_Symbol_pathwayCollection.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/data/wikipwsHS_Symbol_pathwayCollection.rda -------------------------------------------------------------------------------- /docs/404.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/404.html -------------------------------------------------------------------------------- /docs/articles/Introduction_to_pathwayPCA.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/articles/Introduction_to_pathwayPCA.html -------------------------------------------------------------------------------- /docs/articles/Introduction_to_pathwayPCA_files/figure-html/NFKB1SurvPlot-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/articles/Introduction_to_pathwayPCA_files/figure-html/NFKB1SurvPlot-1.png -------------------------------------------------------------------------------- /docs/articles/Introduction_to_pathwayPCA_files/figure-html/NFKB1plot-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/articles/Introduction_to_pathwayPCA_files/figure-html/NFKB1plot-1.png -------------------------------------------------------------------------------- /docs/articles/Introduction_to_pathwayPCA_files/figure-html/graphLoads-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/articles/Introduction_to_pathwayPCA_files/figure-html/graphLoads-1.png -------------------------------------------------------------------------------- /docs/articles/Introduction_to_pathwayPCA_files/figure-html/heatmapWP195-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/articles/Introduction_to_pathwayPCA_files/figure-html/heatmapWP195-1.png -------------------------------------------------------------------------------- /docs/articles/Introduction_to_pathwayPCA_files/figure-html/pathway_bar_plots-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/articles/Introduction_to_pathwayPCA_files/figure-html/pathway_bar_plots-1.png -------------------------------------------------------------------------------- /docs/articles/Introduction_to_pathwayPCA_files/figure-html/plotKidneyGroupedSurv-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/articles/Introduction_to_pathwayPCA_files/figure-html/plotKidneyGroupedSurv-1.png -------------------------------------------------------------------------------- /docs/articles/Introduction_to_pathwayPCA_files/figure-html/unnamed-chunk-1-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/articles/Introduction_to_pathwayPCA_files/figure-html/unnamed-chunk-1-1.png -------------------------------------------------------------------------------- /docs/articles/Introduction_to_pathwayPCA_files/figure-html/wp195PCs-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/articles/Introduction_to_pathwayPCA_files/figure-html/wp195PCs-1.png -------------------------------------------------------------------------------- /docs/articles/Supplement1-Quickstart_Guide.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/articles/Supplement1-Quickstart_Guide.html -------------------------------------------------------------------------------- /docs/articles/Supplement1-Quickstart_Guide_files/figure-html/surv_spr_pval_plot-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/articles/Supplement1-Quickstart_Guide_files/figure-html/surv_spr_pval_plot-1.png -------------------------------------------------------------------------------- /docs/articles/Supplement2-Importing_Data.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/articles/Supplement2-Importing_Data.html -------------------------------------------------------------------------------- /docs/articles/Supplement3-Create_Omics_Objects.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/articles/Supplement3-Create_Omics_Objects.html -------------------------------------------------------------------------------- /docs/articles/Supplement4-Methods_Walkthrough.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/articles/Supplement4-Methods_Walkthrough.html -------------------------------------------------------------------------------- /docs/articles/Supplement5-Analyse_Results.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/articles/Supplement5-Analyse_Results.html -------------------------------------------------------------------------------- /docs/articles/Supplement5-Analyse_Results_files/figure-html/bar_plots-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/articles/Supplement5-Analyse_Results_files/figure-html/bar_plots-1.png -------------------------------------------------------------------------------- /docs/articles/Supplement5-Analyse_Results_files/figure-html/pathway177_correlations_bar_chart-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/articles/Supplement5-Analyse_Results_files/figure-html/pathway177_correlations_bar_chart-1.png -------------------------------------------------------------------------------- /docs/articles/Supplement5-Analyse_Results_files/figure-html/pathway177_loadings_bar_chart-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/articles/Supplement5-Analyse_Results_files/figure-html/pathway177_loadings_bar_chart-1.png -------------------------------------------------------------------------------- /docs/articles/Supplement5-Analyse_Results_files/figure-html/pathway491_correlations_bar_chart-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/articles/Supplement5-Analyse_Results_files/figure-html/pathway491_correlations_bar_chart-1.png -------------------------------------------------------------------------------- /docs/articles/Supplement5-Analyse_Results_files/figure-html/pathway491_loadings_bar_chart-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/articles/Supplement5-Analyse_Results_files/figure-html/pathway491_loadings_bar_chart-1.png -------------------------------------------------------------------------------- /docs/articles/Supplement5-Analyse_Results_files/figure-html/surv_aes_pval_plot-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/articles/Supplement5-Analyse_Results_files/figure-html/surv_aes_pval_plot-1.png -------------------------------------------------------------------------------- /docs/articles/Supplement5-Analyse_Results_files/figure-html/unnamed-chunk-1-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/articles/Supplement5-Analyse_Results_files/figure-html/unnamed-chunk-1-1.png -------------------------------------------------------------------------------- /docs/articles/Supplement5-Analyse_Results_files/figure-html/unnamed-chunk-5-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/articles/Supplement5-Analyse_Results_files/figure-html/unnamed-chunk-5-1.png -------------------------------------------------------------------------------- /docs/articles/circlePlot.PNG: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/articles/circlePlot.PNG -------------------------------------------------------------------------------- /docs/articles/example_assay_data.PNG: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/articles/example_assay_data.PNG -------------------------------------------------------------------------------- /docs/articles/example_pInfo_data.PNG: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/articles/example_pInfo_data.PNG -------------------------------------------------------------------------------- /docs/articles/index.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/articles/index.html -------------------------------------------------------------------------------- /docs/authors.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/authors.html -------------------------------------------------------------------------------- /docs/docsearch.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/docsearch.css -------------------------------------------------------------------------------- /docs/docsearch.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/docsearch.js -------------------------------------------------------------------------------- /docs/docsearch.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/docsearch.json -------------------------------------------------------------------------------- /docs/favicon.ico: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/favicon.ico -------------------------------------------------------------------------------- /docs/index.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/index.html -------------------------------------------------------------------------------- /docs/jquery.sticky-kit.min.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/jquery.sticky-kit.min.js -------------------------------------------------------------------------------- /docs/link.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/link.svg -------------------------------------------------------------------------------- /docs/news/index.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/news/index.html -------------------------------------------------------------------------------- /docs/pkgdown.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/pkgdown.css -------------------------------------------------------------------------------- /docs/pkgdown.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/pkgdown.js -------------------------------------------------------------------------------- /docs/pkgdown.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/pkgdown.yml -------------------------------------------------------------------------------- /docs/reference/AESPCA_pVals.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/reference/AESPCA_pVals.html -------------------------------------------------------------------------------- /docs/reference/CheckAssay.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/reference/CheckAssay.html -------------------------------------------------------------------------------- /docs/reference/CheckPwyColl.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/reference/CheckPwyColl.html -------------------------------------------------------------------------------- /docs/reference/CheckSampleIDs.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/reference/CheckSampleIDs.html -------------------------------------------------------------------------------- /docs/reference/Contains.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/reference/Contains.html -------------------------------------------------------------------------------- /docs/reference/ControlFDR.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/reference/ControlFDR.html -------------------------------------------------------------------------------- /docs/reference/CreateOmics.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/reference/CreateOmics.html -------------------------------------------------------------------------------- /docs/reference/CreateOmicsPathway.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/reference/CreateOmicsPathway.html -------------------------------------------------------------------------------- /docs/reference/CreatePathwayCollection.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/reference/CreatePathwayCollection.html -------------------------------------------------------------------------------- /docs/reference/ExtractAESPCs.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/reference/ExtractAESPCs.html -------------------------------------------------------------------------------- /docs/reference/GumbelMixpValues.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/reference/GumbelMixpValues.html -------------------------------------------------------------------------------- /docs/reference/IntersectOmicsPwyCollct.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/reference/IntersectOmicsPwyCollct.html -------------------------------------------------------------------------------- /docs/reference/JoinPhenoAssay.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/reference/JoinPhenoAssay.html -------------------------------------------------------------------------------- /docs/reference/LoadOntoPCs.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/reference/LoadOntoPCs.html -------------------------------------------------------------------------------- /docs/reference/OmicsCateg-class.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/reference/OmicsCateg-class.html -------------------------------------------------------------------------------- /docs/reference/OmicsPathway-class.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/reference/OmicsPathway-class.html -------------------------------------------------------------------------------- /docs/reference/OmicsReg-class.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/reference/OmicsReg-class.html -------------------------------------------------------------------------------- /docs/reference/OmicsSurv-class.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/reference/OmicsSurv-class.html -------------------------------------------------------------------------------- /docs/reference/OptimGumbelMixParams.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/reference/OptimGumbelMixParams.html -------------------------------------------------------------------------------- /docs/reference/PathwaytValues.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/reference/PathwaytValues.html -------------------------------------------------------------------------------- /docs/reference/PermTestCateg.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/reference/PermTestCateg.html -------------------------------------------------------------------------------- /docs/reference/PermTestReg.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/reference/PermTestReg.html -------------------------------------------------------------------------------- /docs/reference/PermTestSurv.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/reference/PermTestSurv.html -------------------------------------------------------------------------------- /docs/reference/SE2Tidy.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/reference/SE2Tidy.html -------------------------------------------------------------------------------- /docs/reference/SubsetPathwayCollection.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/reference/SubsetPathwayCollection.html -------------------------------------------------------------------------------- /docs/reference/SubsetPathwayData.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/reference/SubsetPathwayData.html -------------------------------------------------------------------------------- /docs/reference/TabulatepValues.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/reference/TabulatepValues.html -------------------------------------------------------------------------------- /docs/reference/TransposeAssay.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/reference/TransposeAssay.html -------------------------------------------------------------------------------- /docs/reference/ValidOmicsSurv.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/reference/ValidOmicsSurv.html -------------------------------------------------------------------------------- /docs/reference/WhichPathways.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/reference/WhichPathways.html -------------------------------------------------------------------------------- /docs/reference/aespca.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/reference/aespca.html -------------------------------------------------------------------------------- /docs/reference/colonSurv_df.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/reference/colonSurv_df.html -------------------------------------------------------------------------------- /docs/reference/colon_pathwayCollection.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/reference/colon_pathwayCollection.html -------------------------------------------------------------------------------- /docs/reference/coxTrain_fun.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/reference/coxTrain_fun.html -------------------------------------------------------------------------------- /docs/reference/getPathPCLs.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/reference/getPathPCLs.html -------------------------------------------------------------------------------- /docs/reference/getPathpVals.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/reference/getPathpVals.html -------------------------------------------------------------------------------- /docs/reference/get_set_OmicsPathway.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/reference/get_set_OmicsPathway.html -------------------------------------------------------------------------------- /docs/reference/get_set_OmicsRegCateg.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/reference/get_set_OmicsRegCateg.html -------------------------------------------------------------------------------- /docs/reference/get_set_OmicsSurv.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/reference/get_set_OmicsSurv.html -------------------------------------------------------------------------------- /docs/reference/glmTrain_fun.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/reference/glmTrain_fun.html -------------------------------------------------------------------------------- /docs/reference/index.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/reference/index.html -------------------------------------------------------------------------------- /docs/reference/lars.lsa.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/reference/lars.lsa.html -------------------------------------------------------------------------------- /docs/reference/mysvd.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/reference/mysvd.html -------------------------------------------------------------------------------- /docs/reference/normalize.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/reference/normalize.html -------------------------------------------------------------------------------- /docs/reference/olsTrain_fun.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/reference/olsTrain_fun.html -------------------------------------------------------------------------------- /docs/reference/pathwayPCA-package.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/reference/pathwayPCA-package.html -------------------------------------------------------------------------------- /docs/reference/pathway_tControl.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/reference/pathway_tControl.html -------------------------------------------------------------------------------- /docs/reference/pathway_tScores.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/reference/pathway_tScores.html -------------------------------------------------------------------------------- /docs/reference/permuteSamps.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/reference/permuteSamps.html -------------------------------------------------------------------------------- /docs/reference/print.pathwayCollection.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/reference/print.pathwayCollection.html -------------------------------------------------------------------------------- /docs/reference/read_gmt.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/reference/read_gmt.html -------------------------------------------------------------------------------- /docs/reference/show-OmicsPathway-method.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/reference/show-OmicsPathway-method.html -------------------------------------------------------------------------------- /docs/reference/superPCA_pVals.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/reference/superPCA_pVals.html -------------------------------------------------------------------------------- /docs/reference/superpc.st.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/reference/superpc.st.html -------------------------------------------------------------------------------- /docs/reference/superpc.train.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/reference/superpc.train.html -------------------------------------------------------------------------------- /docs/reference/wikipwsHS_Entrez_pathwayCollection.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/reference/wikipwsHS_Entrez_pathwayCollection.html -------------------------------------------------------------------------------- /docs/reference/wikipwsHS_Symbol_pathwayCollection.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/reference/wikipwsHS_Symbol_pathwayCollection.html -------------------------------------------------------------------------------- /docs/reference/write_gmt.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/reference/write_gmt.html -------------------------------------------------------------------------------- /docs/sitemap.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/docs/sitemap.xml -------------------------------------------------------------------------------- /inst/extdata/c2.cp.v6.0.symbols.gmt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/inst/extdata/c2.cp.v6.0.symbols.gmt -------------------------------------------------------------------------------- /inst/extdata/ex_assay_subset.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/inst/extdata/ex_assay_subset.csv -------------------------------------------------------------------------------- /inst/extdata/ex_pInfo_subset.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/inst/extdata/ex_pInfo_subset.csv -------------------------------------------------------------------------------- /inst/extdata/wikipathways_human.gmt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/inst/extdata/wikipathways_human.gmt -------------------------------------------------------------------------------- /inst/extdata/wikipathways_human_symbol.gmt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/inst/extdata/wikipathways_human_symbol.gmt -------------------------------------------------------------------------------- /inst/scripts/convert_EntrezID_to_HGNC_Ensembl.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/inst/scripts/convert_EntrezID_to_HGNC_Ensembl.R -------------------------------------------------------------------------------- /inst/scripts/create_airway_example.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/inst/scripts/create_airway_example.R -------------------------------------------------------------------------------- /inst/scripts/generate_ex_subset.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/inst/scripts/generate_ex_subset.R -------------------------------------------------------------------------------- /inst/scripts/import_AP_gmt_20180601.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/inst/scripts/import_AP_gmt_20180601.R -------------------------------------------------------------------------------- /inst/scripts/issue_65_20220222.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/inst/scripts/issue_65_20220222.R -------------------------------------------------------------------------------- /inst/scripts/multi_pathway_overlap_fishers.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/inst/scripts/multi_pathway_overlap_fishers.R -------------------------------------------------------------------------------- /man/AESPCA_pVals.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/man/AESPCA_pVals.Rd -------------------------------------------------------------------------------- /man/CheckAssay.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/man/CheckAssay.Rd -------------------------------------------------------------------------------- /man/CheckPwyColl.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/man/CheckPwyColl.Rd -------------------------------------------------------------------------------- /man/CheckSampleIDs.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/man/CheckSampleIDs.Rd -------------------------------------------------------------------------------- /man/Contains.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/man/Contains.Rd -------------------------------------------------------------------------------- /man/ControlFDR.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/man/ControlFDR.Rd -------------------------------------------------------------------------------- /man/CreateOmics.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/man/CreateOmics.Rd -------------------------------------------------------------------------------- /man/CreateOmicsPathway.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/man/CreateOmicsPathway.Rd -------------------------------------------------------------------------------- /man/CreatePathwayCollection.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/man/CreatePathwayCollection.Rd -------------------------------------------------------------------------------- /man/ExtractAESPCs.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/man/ExtractAESPCs.Rd -------------------------------------------------------------------------------- /man/GumbelMixpValues.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/man/GumbelMixpValues.Rd -------------------------------------------------------------------------------- /man/IntersectOmicsPwyCollct.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/man/IntersectOmicsPwyCollct.Rd -------------------------------------------------------------------------------- /man/JoinPhenoAssay.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/man/JoinPhenoAssay.Rd -------------------------------------------------------------------------------- /man/LoadOntoPCs.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/man/LoadOntoPCs.Rd -------------------------------------------------------------------------------- /man/OmicsCateg-class.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/man/OmicsCateg-class.Rd -------------------------------------------------------------------------------- /man/OmicsPathway-class.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/man/OmicsPathway-class.Rd -------------------------------------------------------------------------------- /man/OmicsReg-class.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/man/OmicsReg-class.Rd -------------------------------------------------------------------------------- /man/OmicsSurv-class.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/man/OmicsSurv-class.Rd -------------------------------------------------------------------------------- /man/OptimGumbelMixParams.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/man/OptimGumbelMixParams.Rd -------------------------------------------------------------------------------- /man/PathwaytValues.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/man/PathwaytValues.Rd -------------------------------------------------------------------------------- /man/PermTestCateg.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/man/PermTestCateg.Rd -------------------------------------------------------------------------------- /man/PermTestReg.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/man/PermTestReg.Rd -------------------------------------------------------------------------------- /man/PermTestSurv.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/man/PermTestSurv.Rd -------------------------------------------------------------------------------- /man/SE2Tidy.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/man/SE2Tidy.Rd -------------------------------------------------------------------------------- /man/SubsetPathwayCollection.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/man/SubsetPathwayCollection.Rd -------------------------------------------------------------------------------- /man/SubsetPathwayData.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/man/SubsetPathwayData.Rd -------------------------------------------------------------------------------- /man/SuperPCA_pVals.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/man/SuperPCA_pVals.Rd -------------------------------------------------------------------------------- /man/TabulatepValues.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/man/TabulatepValues.Rd -------------------------------------------------------------------------------- /man/TransposeAssay.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/man/TransposeAssay.Rd -------------------------------------------------------------------------------- /man/ValidOmicsSurv.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/man/ValidOmicsSurv.Rd -------------------------------------------------------------------------------- /man/WhichPathways.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/man/WhichPathways.Rd -------------------------------------------------------------------------------- /man/aespca.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/man/aespca.Rd -------------------------------------------------------------------------------- /man/colonSurv_df.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/man/colonSurv_df.Rd -------------------------------------------------------------------------------- /man/colon_pathwayCollection.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/man/colon_pathwayCollection.Rd -------------------------------------------------------------------------------- /man/coxTrain_fun.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/man/coxTrain_fun.Rd -------------------------------------------------------------------------------- /man/getPathPCLs.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/man/getPathPCLs.Rd -------------------------------------------------------------------------------- /man/getPathpVals.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/man/getPathpVals.Rd -------------------------------------------------------------------------------- /man/get_set_OmicsPathway.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/man/get_set_OmicsPathway.Rd -------------------------------------------------------------------------------- /man/get_set_OmicsRegCateg.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/man/get_set_OmicsRegCateg.Rd -------------------------------------------------------------------------------- /man/get_set_OmicsSurv.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/man/get_set_OmicsSurv.Rd -------------------------------------------------------------------------------- /man/glmTrain_fun.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/man/glmTrain_fun.Rd -------------------------------------------------------------------------------- /man/lars.lsa.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/man/lars.lsa.Rd -------------------------------------------------------------------------------- /man/mysvd.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/man/mysvd.Rd -------------------------------------------------------------------------------- /man/normalize.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/man/normalize.Rd -------------------------------------------------------------------------------- /man/olsTrain_fun.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/man/olsTrain_fun.Rd -------------------------------------------------------------------------------- /man/pathwayPCA-package.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/man/pathwayPCA-package.Rd -------------------------------------------------------------------------------- /man/pathway_tControl.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/man/pathway_tControl.Rd -------------------------------------------------------------------------------- /man/pathway_tScores.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/man/pathway_tScores.Rd -------------------------------------------------------------------------------- /man/permuteSamps.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/man/permuteSamps.Rd -------------------------------------------------------------------------------- /man/print.pathwayCollection.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/man/print.pathwayCollection.Rd -------------------------------------------------------------------------------- /man/read_gmt.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/man/read_gmt.Rd -------------------------------------------------------------------------------- /man/show-OmicsPathway-method.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/man/show-OmicsPathway-method.Rd -------------------------------------------------------------------------------- /man/superpc.st.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/man/superpc.st.Rd -------------------------------------------------------------------------------- /man/superpc.train.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/man/superpc.train.Rd -------------------------------------------------------------------------------- /man/wikipwsHS_Entrez_pathwayCollection.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/man/wikipwsHS_Entrez_pathwayCollection.Rd -------------------------------------------------------------------------------- /man/wikipwsHS_Symbol_pathwayCollection.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/man/wikipwsHS_Symbol_pathwayCollection.Rd -------------------------------------------------------------------------------- /man/write_gmt.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/man/write_gmt.Rd -------------------------------------------------------------------------------- /tests/testthat.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/tests/testthat.R -------------------------------------------------------------------------------- /tests/testthat/test_AESPCA_pVals.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/tests/testthat/test_AESPCA_pVals.R -------------------------------------------------------------------------------- /tests/testthat/test_Contains.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/tests/testthat/test_Contains.R -------------------------------------------------------------------------------- /tests/testthat/test_CreateOmicsWrapper.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/tests/testthat/test_CreateOmicsWrapper.R -------------------------------------------------------------------------------- /tests/testthat/test_CreatePathwayCollection.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/tests/testthat/test_CreatePathwayCollection.R -------------------------------------------------------------------------------- /tests/testthat/test_LoadOntoPCs.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/tests/testthat/test_LoadOntoPCs.R -------------------------------------------------------------------------------- /tests/testthat/test_SE2Tidy.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/tests/testthat/test_SE2Tidy.R -------------------------------------------------------------------------------- /tests/testthat/test_SubsetPathwayData.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/tests/testthat/test_SubsetPathwayData.R -------------------------------------------------------------------------------- /tests/testthat/test_SuperPCA_pVals.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/tests/testthat/test_SuperPCA_pVals.R -------------------------------------------------------------------------------- /tests/testthat/test_WhichPathways.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/tests/testthat/test_WhichPathways.R -------------------------------------------------------------------------------- /tests/testthat/test_getPathPCLs.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/tests/testthat/test_getPathPCLs.R -------------------------------------------------------------------------------- /tests/testthat/test_getPathpVals.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/tests/testthat/test_getPathpVals.R -------------------------------------------------------------------------------- /tests/testthat/test_read_gmt.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/tests/testthat/test_read_gmt.R -------------------------------------------------------------------------------- /tests/testthat/test_write_gmt.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/tests/testthat/test_write_gmt.R -------------------------------------------------------------------------------- /vignettes/Introduction_to_pathwayPCA.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/vignettes/Introduction_to_pathwayPCA.Rmd -------------------------------------------------------------------------------- /vignettes/Supplement1-Quickstart_Guide.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/vignettes/Supplement1-Quickstart_Guide.Rmd -------------------------------------------------------------------------------- /vignettes/Supplement2-Importing_Data.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/vignettes/Supplement2-Importing_Data.Rmd -------------------------------------------------------------------------------- /vignettes/Supplement3-Create_Omics_Objects.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/vignettes/Supplement3-Create_Omics_Objects.Rmd -------------------------------------------------------------------------------- /vignettes/Supplement4-Methods_Walkthrough.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/vignettes/Supplement4-Methods_Walkthrough.Rmd -------------------------------------------------------------------------------- /vignettes/Supplement5-Analyse_Results.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/vignettes/Supplement5-Analyse_Results.Rmd -------------------------------------------------------------------------------- /vignettes/circlePlot.PNG: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/vignettes/circlePlot.PNG -------------------------------------------------------------------------------- /vignettes/circlePlotData.RDS: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/vignettes/circlePlotData.RDS -------------------------------------------------------------------------------- /vignettes/example_assay_data.PNG: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/vignettes/example_assay_data.PNG -------------------------------------------------------------------------------- /vignettes/example_pInfo_data.PNG: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gabrielodom/pathwayPCA/HEAD/vignettes/example_pInfo_data.PNG --------------------------------------------------------------------------------