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_pathwayCollection_which.R R/accessClass_pcOut.R R/accessClass_pcOutpVals.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/data_wikipathways_symbols.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_pathway_tValues.R R/superPC_permuteSamples.R R/superPC_wrapper.R R/utils_Contains.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_stdExpr_2_tidyAssay.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

data/wikipwsHS_Symbol_pathwayCollection.rda

docs/404.html

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/heatmapWP195-1.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/Supplement5-Analyse_Results_files/figure-html/unnamed-chunk-5-1.png

docs/articles/circlePlot.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/Contains.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/PathwaytValues.html

docs/reference/PermTestCateg.html

docs/reference/PermTestReg.html

docs/reference/PermTestSurv.html

docs/reference/SE2Tidy.html

docs/reference/SubsetPathwayCollection.html

docs/reference/SubsetPathwayData.html

docs/reference/TabulatepValues.html

docs/reference/TransposeAssay.html

docs/reference/ValidOmicsSurv.html

docs/reference/WhichPathways.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/getPathpVals.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/wikipwsHS_Symbol_pathwayCollection.html

docs/reference/write_gmt.html

docs/sitemap.xml

inst/extdata/c2.cp.v6.0.symbols.gmt

inst/extdata/ex_assay_subset.csv

inst/extdata/ex_pInfo_subset.csv

inst/extdata/wikipathways_human.gmt

inst/extdata/wikipathways_human_symbol.gmt

vignettes/circlePlot.PNG

vignettes/circlePlotData.RDS

vignettes/example_assay_data.PNG

vignettes/example_pInfo_data.PNG

gabrielodom/pathwayPCA documentation built on July 10, 2023, 3:32 a.m.

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

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Integrative Pathway Analysis with Modern PCA Methodology and Gene Selection

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

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

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