Files in gabrielodom/pathwayPCA
Integrative Pathway Analysis with Modern PCA Methodology and Gene Selection

.Rbuildignore
.gitignore
.travis.yml
DESCRIPTION
NAMESPACE
NEWS.md R/CreatePathwayCollection.R R/accessClass_OmicsPath.R R/accessClass_OmicsPathData.R R/accessClass_OmicsRegCateg.R R/accessClass_OmicsSurv.R R/accessClass_pathwayCollection.R R/accessClass_pcOut.R R/aesPC_calculate_AESPCA.R R/aesPC_calculate_LARS.R R/aesPC_extract_OmicsPath_PCs.R R/aesPC_permtest_CoxPH.R R/aesPC_permtest_GLM.R R/aesPC_permtest_LM.R R/aesPC_unknown_matrixNorm.R R/aesPC_wrapper.R R/createClass_OmicsCateg.R R/createClass_OmicsPath.R R/createClass_OmicsReg.R R/createClass_OmicsSurv.R R/createClass_validOmics.R R/createOmics_All.R R/createOmics_CheckAssay.R R/createOmics_CheckPathwayCollection.R R/createOmics_CheckSampleIDs.R R/createOmics_JoinPhenoAssay.R R/createOmics_TrimPathwayCollection.R R/createOmics_Wrapper.R R/data_colonSubset.R R/data_genesetSubset.R R/data_wikipathways.R R/pathwayPCA.R R/printClass_Omics_All.R R/printClass_pathwayCollection.R R/superPC_model_CoxPH.R R/superPC_model_GLM.R R/superPC_model_LS.R R/superPC_model_tStats.R R/superPC_model_train.R R/superPC_modifiedSVD.R R/superPC_optimWeibullParams.R R/superPC_optimWeibull_pValues.R R/superPC_pathway_tControl.R R/superPC_pathway_tScores.R R/superPC_permuteSamples.R R/superPC_wrapper.R R/utils_adjust_and_sort_pValues.R R/utils_load_test_data_onto_PCs.R R/utils_multtest_pvalues.R R/utils_read_gmt.R R/utils_transpose_assay.R R/utils_write_gmt.R README.md
_pkgdown.yaml
data/colonSurv_df.rda
data/colon_pathwayCollection.rda
data/wikipwsHS_Entrez_pathwayCollection.rda
docs/articles/Introduction_to_pathwayPCA.html
docs/articles/Introduction_to_pathwayPCA_files/figure-html/NFKB1SurvPlot-1.png
docs/articles/Introduction_to_pathwayPCA_files/figure-html/NFKB1plot-1.png
docs/articles/Introduction_to_pathwayPCA_files/figure-html/graphLoads-1.png
docs/articles/Introduction_to_pathwayPCA_files/figure-html/pathway_bar_plots-1.png
docs/articles/Introduction_to_pathwayPCA_files/figure-html/plotKidneyGroupedSurv-1.png
docs/articles/Introduction_to_pathwayPCA_files/figure-html/unnamed-chunk-1-1.png
docs/articles/Introduction_to_pathwayPCA_files/figure-html/wp195PCs-1.png
docs/articles/Supplement1-Quickstart_Guide.html
docs/articles/Supplement1-Quickstart_Guide_files/figure-html/surv_spr_pval_plot-1.png
docs/articles/Supplement2-Importing_Data.html
docs/articles/Supplement3-Create_Omics_Objects.html
docs/articles/Supplement4-Methods_Walkthrough.html
docs/articles/Supplement5-Analyse_Results.html
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
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
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
docs/articles/Supplement5-Analyse_Results_files/figure-html/unnamed-chunk-1-1.png
docs/articles/circlePlot.PNG
docs/articles/circosPlot.PNG
docs/articles/example_assay_data.PNG
docs/articles/example_pInfo_data.PNG
docs/articles/index.html
docs/authors.html
docs/docsearch.css
docs/docsearch.js
docs/docsearch.json
docs/favicon.ico
docs/index.html
docs/jquery.sticky-kit.min.js
docs/link.svg
docs/news/index.html
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/AESPCA_pVals.html
docs/reference/CheckAssay.html
docs/reference/CheckPwyColl.html
docs/reference/CheckSampleIDs.html
docs/reference/ControlFDR.html
docs/reference/CreateOmics.html
docs/reference/CreateOmicsPathway.html
docs/reference/CreatePathwayCollection.html
docs/reference/ExtractAESPCs.html
docs/reference/GumbelMixpValues.html
docs/reference/IntersectOmicsPwyCollct.html
docs/reference/JoinPhenoAssay.html
docs/reference/LoadOntoPCs.html
docs/reference/OmicsCateg-class.html
docs/reference/OmicsPathway-class.html
docs/reference/OmicsReg-class.html
docs/reference/OmicsSurv-class.html
docs/reference/OptimGumbelMixParams.html
docs/reference/PermTestCateg.html
docs/reference/PermTestReg.html
docs/reference/PermTestSurv.html
docs/reference/SubsetPathwayCollection.html
docs/reference/SubsetPathwayData.html
docs/reference/SuperPCA_pVals.html
docs/reference/TabulatepValues.html
docs/reference/TransposeAssay.html
docs/reference/ValidOmicsSurv.html
docs/reference/aespca.html
docs/reference/colonSurv_df.html
docs/reference/colon_pathwayCollection.html
docs/reference/coxTrain_fun.html
docs/reference/getPathPCLs.html
docs/reference/get_set_OmicsPathway.html
docs/reference/get_set_OmicsRegCateg.html
docs/reference/get_set_OmicsSurv.html
docs/reference/glmTrain_fun.html
docs/reference/index.html
docs/reference/lars.lsa.html
docs/reference/mysvd.html
docs/reference/normalize.html
docs/reference/olsTrain_fun.html
docs/reference/pathwayPCA-package.html
docs/reference/pathway_tControl.html
docs/reference/pathway_tScores.html
docs/reference/permuteSamps.html
docs/reference/print.pathwayCollection.html
docs/reference/read_gmt.html
docs/reference/show-OmicsPathway-method.html
docs/reference/superPCA_pVals.html
docs/reference/superpc.st.html
docs/reference/superpc.train.html
docs/reference/wikipwsHS_Entrez_pathwayCollection.html
docs/reference/write_gmt.html
docs/sitemap.xml
inst/extdata/KIRP_Surv_RNAseq_inner.RDS
inst/extdata/OV_surv_x_CNV2.RDS
inst/extdata/c2.cp.v6.0.symbols.gmt
inst/extdata/ex_assay_subset.csv
inst/extdata/ex_pInfo_subset.csv
inst/extdata/generate_ex_subset.R inst/extdata/import_AP_gmt_20180601.R
inst/extdata/ovarian_PNNL_survival.RDS
inst/extdata/wikipathways_human.gmt
inst/extdata/wikipathways_human_symbol.gmt
inst/misc_scripts/Roxygen_Template_Function.R inst/misc_scripts/calculate_gene_rank.R inst/misc_scripts/superPC_pathway_pValues.R inst/misc_scripts/utils_matrixRoot.R
inst/pkgdown_yaml_options.txt
inst/vignette_docx/C1-Quickstart_Guide.docx
inst/vignette_docx/C1-Quickstart_Guide_20180427.docx
inst/vignette_docx/C1-Quickstart_Guide_20180430.docx
inst/vignette_docx/C1-Quickstart_Guide_20180501.docx
inst/vignette_docx/C1-Quickstart_Guide_LWedit.docx
inst/vignette_docx/C2-Importing_Data.docx
inst/vignette_docx/C2-Importing_Data_20180427.docx
inst/vignette_docx/C3-Create_Omics_Objects.docx
inst/vignette_docx/C3-Create_Omics_Objects_20180427.docx
inst/vignette_docx/C4-Methods_Walkthrough.docx
inst/vignette_docx/C4-Methods_Walkthrough_20180427.docx
inst/vignette_drafts/Package_Dev_Notes.Rmd inst/vignette_drafts/Supervised_PCA_Walkthrough.Rmd
inst/vignette_drafts/aespcaOut_20181009.RDS
inst/vignette_drafts/pathwayPCA_Users_Guide.Rmd man/AESPCA_pVals.Rd man/CheckAssay.Rd man/CheckPwyColl.Rd man/CheckSampleIDs.Rd man/ControlFDR.Rd man/CreateOmics.Rd man/CreateOmicsPathway.Rd man/CreatePathwayCollection.Rd man/ExtractAESPCs.Rd man/GumbelMixpValues.Rd man/IntersectOmicsPwyCollct.Rd man/JoinPhenoAssay.Rd man/LoadOntoPCs.Rd man/OmicsCateg-class.Rd man/OmicsPathway-class.Rd man/OmicsReg-class.Rd man/OmicsSurv-class.Rd man/OptimGumbelMixParams.Rd man/PermTestCateg.Rd man/PermTestReg.Rd man/PermTestSurv.Rd man/SubsetPathwayCollection.Rd man/SubsetPathwayData.Rd man/SuperPCA_pVals.Rd man/TabulatepValues.Rd man/TransposeAssay.Rd man/ValidOmicsSurv.Rd man/aespca.Rd man/colonSurv_df.Rd man/colon_pathwayCollection.Rd man/coxTrain_fun.Rd man/getPathPCLs.Rd man/get_set_OmicsPathway.Rd man/get_set_OmicsRegCateg.Rd man/get_set_OmicsSurv.Rd man/glmTrain_fun.Rd man/lars.lsa.Rd man/mysvd.Rd man/normalize.Rd man/olsTrain_fun.Rd man/pathwayPCA-package.Rd man/pathway_tControl.Rd man/pathway_tScores.Rd man/permuteSamps.Rd man/print.pathwayCollection.Rd man/read_gmt.Rd man/show-OmicsPathway-method.Rd man/superpc.st.Rd man/superpc.train.Rd man/wikipwsHS_Entrez_pathwayCollection.Rd man/write_gmt.Rd
pathwayPCA.Rproj
pathwayPCA.pdf testing_files/James_Tests_20180228.Rmd testing_files/Test_Graphics_v2.R testing_files/Test_GraphicsforAdjustedpValues.R testing_files/Test_JoinPhenoAssay.R testing_files/Test_Omics_accessor_functions.R testing_files/Test_Passing_Function_as_Argument.R testing_files/Test_PermTestCateg_Parametric.R testing_files/Test_PermTestReg_Parametric.R testing_files/Test_PermTestSurv_Parametric.R testing_files/Test_PermutationTest_Benchmark.R testing_files/Test_ResponseConversion.R testing_files/Test_S4_and_S3_print_show_methods.R testing_files/Test_SVD_package_options.R testing_files/Test_accessClass_pathwayCollection.R testing_files/Test_aespca.R testing_files/Test_createPathwaySet.R testing_files/Test_create_OmicsWrapper.R testing_files/Test_getPathSVD.R testing_files/Test_proper_gene_names.R testing_files/Test_read_gmt.R testing_files/Test_supervisedPCA_classification.R testing_files/Test_supervisedPCA_regression.R testing_files/Test_supervisedPCA_survival.R testing_files/Test_supervisedPCA_wrapper.R testing_files/Test_supervised_pValueAdjust.R testing_files/Test_topGenes.R testing_files/Testing_S4.R testing_files/aes-pca_raw_functions.R testing_files/benchmark_svd.R
testing_files/superpc.txt
vignettes/Introduction_to_pathwayPCA.Rmd
vignettes/KIRP_protein_aespcOut.RDS
vignettes/Supplement1-Quickstart_Guide.Rmd vignettes/Supplement2-Importing_Data.Rmd vignettes/Supplement3-Create_Omics_Objects.Rmd vignettes/Supplement4-Methods_Walkthrough.Rmd vignettes/Supplement5-Analyse_Results.Rmd
vignettes/circlePlot.PNG
vignettes/circlePlotData.RDS
vignettes/example_assay_data.PNG
vignettes/example_pInfo_data.PNG
vignettes/ovarian_copyNum_aespcOut.RDS
gabrielodom/pathwayPCA documentation built on Jan. 10, 2019, 9:39 p.m.