Files in gabrielodom/pathwayPCA
Test Pathways for Statistically Significant Relationships

.Rbuildignore
.gitignore
.travis.yml
DESCRIPTION
NAMESPACE
NEWS.md R/accessClass_OmicsPath.R R/accessClass_OmicsRegCateg.R R/accessClass_OmicsSurv.R R/adjust_and_sort_pValues.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_LS.R R/aesPC_unknown_matrixNorm.R R/aesPC_wrapper.R R/calculate_gene_rank.R R/calculate_matrixRoot.R R/calculate_multtest_pvalues.R R/createClass_OmicsCateg.R R/createClass_OmicsPath.R R/createClass_OmicsReg.R R/createClass_OmicsSurv.R R/createClass_validOmics.R R/create_Omics_All.R R/create_Omics_Wrapper.R R/create_pathwaySet.R R/data_colonSubset.R R/data_genesetSubset.R R/printClass_Omics_All.R R/printClass_pathwaySet.R R/read_gmt.R R/subsetExpressed-omes.R R/superPC_model_CoxPH.R R/superPC_model_GLM.R R/superPC_model_LS.R R/superPC_model_tStats.R R/superPC_modifiedSVD.R R/superPC_optimWeibullParams.R R/superPC_optimWeibull_pValues.R R/superPC_pathway_pValues.R R/superPC_pathway_tControl.R R/superPC_pathway_tScores.R R/superPC_permuteSamples.R R/superPC_train.R R/superPC_wrapper.R R/transpose_assay.R README.Rmd
README.html
_pkgdown.yaml
data/colonSurv_df.rda
data/colon_pathwaySet.rda
docs/articles/C1-Quickstart_Guide.html
docs/articles/C1-Quickstart_Guide_files/figure-html/surv_spr_pval_plot-1.png
docs/articles/C2-Importing_Data.html
docs/articles/C3-Create_Omics_Objects.html
docs/articles/C4-Methods_Walkthrough.html
docs/articles/C4-Methods_Walkthrough_files/figure-html/surv_aes_pval_plot-1.png
docs/articles/C4-Methods_Walkthrough_files/figure-html/surv_spr_pval_plot-1.png
docs/articles/Package_Dev_Notes.html
docs/articles/example_assay_data.PNG
docs/articles/example_pInfo_data.PNG
docs/articles/index.html
docs/authors.html
docs/docsearch.json
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/OmicsCateg-class.html
docs/reference/OmicsPathway-class.html
docs/reference/OmicsReg-class.html
docs/reference/OmicsSurv-class.html
docs/reference/adjustRaw_pVals.html
docs/reference/adjust_and_sort.html
docs/reference/aespca.html
docs/reference/colonGenesets_ls.html
docs/reference/colonSurv_df.html
docs/reference/colon_pathwaySet.html
docs/reference/coxTrain_fun.html
docs/reference/create_Omics.html
docs/reference/create_OmicsPathway.html
docs/reference/create_pathwaySet.html
docs/reference/expressedOmes.html
docs/reference/extract_aesPCs.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/matrixRoot.html
docs/reference/mysvd.html
docs/reference/normalize.html
docs/reference/olsTrain_fun.html
docs/reference/pathway_pValues.html
docs/reference/pathway_tControl.html
docs/reference/pathway_tScores.html
docs/reference/permTest_OmicsCateg.html
docs/reference/permTest_OmicsReg.html
docs/reference/permTest_OmicsSurv.html
docs/reference/permuteSamps.html
docs/reference/print.pathwaySet.html
docs/reference/randomControlSample.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/topGenes.html
docs/reference/transpose_assay.html
docs/reference/valid_OmicsSurv.html
docs/reference/weibullMix_optimParams.html
docs/reference/weibullMix_pValues.html
docs/sitemap.xml
inst/Supervised_PCA_Walkthrough.Rmd
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/pkgdown_yaml_options.txt
inst/vignette_docx/C1-Quickstart_Guide.docx
inst/vignette_docx/C2-Importing_Data.docx
inst/vignette_docx/C3-Create_Omics_Objects.docx
inst/vignette_docx/C4-Methods_Walkthrough.docx
man/AESPCA_pVals.Rd man/OmicsCateg-class.Rd man/OmicsPathway-class.Rd man/OmicsReg-class.Rd man/OmicsSurv-class.Rd man/adjustRaw_pVals.Rd man/adjust_and_sort.Rd man/aespca.Rd man/colonSurv_df.Rd man/colon_pathwaySet.Rd man/coxTrain_fun.Rd man/create_Omics.Rd man/create_OmicsPathway.Rd man/create_pathwaySet.Rd man/expressedOmes.Rd man/extract_aesPCs.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/matrixRoot.Rd man/mysvd.Rd man/normalize.Rd man/olsTrain_fun.Rd man/pathway_pValues.Rd man/pathway_tControl.Rd man/pathway_tScores.Rd man/permTest_OmicsCateg.Rd man/permTest_OmicsReg.Rd man/permTest_OmicsSurv.Rd man/permuteSamps.Rd man/print.pathwaySet.Rd man/read_gmt.Rd man/show-OmicsPathway-method.Rd man/superPCA_pVals.Rd man/superpc.st.Rd man/superpc.train.Rd man/topGenes.Rd man/transpose_assay.Rd man/valid_OmicsSurv.Rd man/weibullMix_optimParams.Rd man/weibullMix_pValues.Rd
pathwayPCA.Rproj
pathwayPCA.pdf testing_files/James_Tests_20180228.Rmd
testing_files/James_Tests_20180228.html
testing_files/Roxygen_Template_Function.R testing_files/Test_Graphics_v2.R testing_files/Test_GraphicsforAdjustedpValues.R testing_files/Test_Omics_accessor_functions.R testing_files/Test_Passing_Function_as_Argument.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_aespca.R testing_files/Test_createPathwaySet.R testing_files/Test_create_OmicsWrapper.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/superpc.txt
vignettes/C1-Quickstart_Guide.Rmd vignettes/C2-Importing_Data.Rmd vignettes/C3-Create_Omics_Objects.Rmd vignettes/C4-Methods_Walkthrough.Rmd vignettes/Package_Dev_Notes.Rmd
vignettes/example_assay_data.PNG
vignettes/example_pInfo_data.PNG
gabrielodom/pathwayPCA documentation built on April 23, 2018, 1:10 p.m.