Files in pathwayPCA

Integrative Pathway Analysis with Modern PCA Methodology and Gene Selection

NEWS.md README.md tests/testthat.R tests/testthat/test_AESPCA_pVals.R tests/testthat/test_CreateOmicsWrapper.R tests/testthat/test_LoadOntoPCs.R tests/testthat/test_SuperPCA_pVals.R tests/testthat/test_SubsetPathwayData.R tests/testthat/test_SE2Tidy.R tests/testthat/test_write_gmt.R tests/testthat/test_CreatePathwayCollection.R tests/testthat/test_getPathPCLs.R tests/testthat/test_getPathpVals.R tests/testthat/test_WhichPathways.R tests/testthat/test_read_gmt.R tests/testthat/test_Contains.R R/utils_read_gmt.R R/aesPC_calculate_LARS.R R/superPC_optimWeibullParams.R R/aesPC_calculate_AESPCA.R R/accessClass_OmicsPathData.R R/createOmics_Wrapper.R R/createOmics_All.R R/createOmics_JoinPhenoAssay.R R/accessClass_pathwayCollection_which.R R/aesPC_permtest_CoxPH.R R/CreatePathwayCollection.R R/superPC_optimWeibull_pValues.R R/createOmics_CheckAssay.R R/superPC_pathway_tValues.R R/accessClass_OmicsSurv.R R/superPC_model_GLM.R R/utils_Contains.R R/data_genesetSubset.R R/utils_multtest_pvalues.R R/printClass_pathwayCollection.R R/superPC_permuteSamples.R R/aesPC_wrapper.R R/utils_transpose_assay.R R/createClass_OmicsPath.R R/createOmics_CheckPathwayCollection.R R/aesPC_permtest_GLM.R R/createClass_OmicsReg.R R/superPC_wrapper.R R/superPC_model_LS.R R/aesPC_extract_OmicsPath_PCs.R R/data_wikipathways.R R/utils_adjust_and_sort_pValues.R R/utils_load_test_data_onto_PCs.R R/accessClass_pathwayCollection.R R/createClass_OmicsSurv.R R/aesPC_unknown_matrixNorm.R R/superPC_model_tStats.R R/pathwayPCA.R R/utils_write_gmt.R R/accessClass_pcOutpVals.R R/data_colonSubset.R R/createClass_OmicsCateg.R R/accessClass_OmicsRegCateg.R R/superPC_model_CoxPH.R R/superPC_pathway_tControl.R R/superPC_pathway_tScores.R R/createClass_validOmics.R R/superPC_model_train.R R/utils_stdExpr_2_tidyAssay.R R/createOmics_CheckSampleIDs.R R/superPC_modifiedSVD.R R/accessClass_pcOut.R R/createOmics_TrimPathwayCollection.R R/data_wikipathways_symbols.R R/accessClass_OmicsPath.R R/printClass_Omics_All.R R/aesPC_permtest_LM.R man/ExtractAESPCs.Rd man/get_set_OmicsPathway.Rd man/mysvd.Rd man/IntersectOmicsPwyCollct.Rd man/olsTrain_fun.Rd man/OmicsSurv-class.Rd man/JoinPhenoAssay.Rd man/OptimGumbelMixParams.Rd man/AESPCA_pVals.Rd man/CheckPwyColl.Rd man/getPathPCLs.Rd man/PathwaytValues.Rd man/get_set_OmicsSurv.Rd man/permuteSamps.Rd man/CheckAssay.Rd man/PermTestSurv.Rd man/PermTestReg.Rd man/colon_pathwayCollection.Rd man/LoadOntoPCs.Rd man/aespca.Rd man/OmicsReg-class.Rd man/SuperPCA_pVals.Rd man/read_gmt.Rd man/TabulatepValues.Rd man/pathway_tControl.Rd man/pathwayPCA-package.Rd man/pathway_tScores.Rd man/glmTrain_fun.Rd man/CreatePathwayCollection.Rd man/SE2Tidy.Rd man/get_set_OmicsRegCateg.Rd man/OmicsCateg-class.Rd man/ControlFDR.Rd man/getPathpVals.Rd man/PermTestCateg.Rd man/print.pathwayCollection.Rd man/normalize.Rd man/CreateOmics.Rd man/CheckSampleIDs.Rd man/ValidOmicsSurv.Rd man/show-OmicsPathway-method.Rd man/wikipwsHS_Entrez_pathwayCollection.Rd man/colonSurv_df.Rd man/OmicsPathway-class.Rd man/Contains.Rd man/write_gmt.Rd man/CreateOmicsPathway.Rd man/coxTrain_fun.Rd man/superpc.train.Rd man/wikipwsHS_Symbol_pathwayCollection.Rd man/superpc.st.Rd man/SubsetPathwayData.Rd man/TransposeAssay.Rd man/lars.lsa.Rd man/SubsetPathwayCollection.Rd man/WhichPathways.Rd man/GumbelMixpValues.Rd inst/doc/Supplement1-Quickstart_Guide.Rmd inst/doc/Introduction_to_pathwayPCA.Rmd inst/doc/Supplement1-Quickstart_Guide.R inst/doc/Supplement3-Create_Omics_Objects.Rmd inst/doc/Supplement4-Methods_Walkthrough.Rmd inst/doc/Supplement4-Methods_Walkthrough.R inst/doc/Supplement2-Importing_Data.Rmd inst/doc/Supplement3-Create_Omics_Objects.R inst/doc/Supplement2-Importing_Data.R inst/doc/Supplement5-Analyse_Results.Rmd inst/doc/Supplement5-Analyse_Results.R inst/doc/Introduction_to_pathwayPCA.R inst/scripts/generate_ex_subset.R inst/scripts/create_airway_example.R inst/scripts/convert_EntrezID_to_HGNC_Ensembl.R inst/scripts/multi_pathway_overlap_fishers.R inst/scripts/import_AP_gmt_20180601.R vignettes/Supplement1-Quickstart_Guide.Rmd vignettes/Introduction_to_pathwayPCA.Rmd vignettes/Supplement3-Create_Omics_Objects.Rmd vignettes/Supplement4-Methods_Walkthrough.Rmd vignettes/Supplement2-Importing_Data.Rmd vignettes/Supplement5-Analyse_Results.Rmd