aespca                  Adaptive, elastic-net, sparse principal
                        component analysis
AESPCA_pVals            Test pathway association with AES-PCA
colon_pathwayCollection
                        Gene Pathway Subset
colonSurv_df            Colon Cancer -Omics Data
Contains                Check if a long atomic vector contains a short
                        atomic vector
CreateOmics             Generation Wrapper function for '-Omics*'-class
                        objects
CreateOmicsPath         Generation functions for '-Omics*'-class
                        objects
CreatePathwayCollection
                        Manually Create a 'pathwayCollection'-class
                        Object.
getPathPCLs             Extract PCs and Loadings from a 'superpcOut'-
                        or 'aespcOut'-class Object.
getPathpVals            Extract Table of p-values from a 'superpcOut'-
                        or 'aespcOut'- class Object.
LoadOntoPCs             Calculate Test Data PCs from Training-Data
                        Estimated Loadings
OmicsCateg-class        An S4 class for categorical responses within an
                        'OmicsPathway' object
OmicsPathway-class      An S4 class for mass spectrometry or bio-assay
                        data and gene pathway lists
OmicsReg-class          An S4 class for continuous responses within an
                        'OmicsPathway' object
OmicsSurv-class         An S4 class for survival responses within an
                        'OmicsPathway' object
pathwayPCA              Extract and Test the Significance of
                        Pathway-Specific Principal Components
read_gmt                Read a '.gmt' file in as a 'pathwayCollection'
                        object
SE2Tidy                 Tidy a SummarizedExperiment Assay
SubsetOmicsPath         Access and Edit Assay or 'pathwayCollection'
                        Values in 'Omics*' Objects
SubsetOmicsResponse     Access and Edit Response of an 'OmicsReg' or
                        'OmicsReg' Object
SubsetOmicsSurv         Access and Edit Event Time or Indicator in an
                        'OmicsSurv' Object
SubsetPathwayCollection
                        Subset a 'pathwayCollection'-class Object by
                        Pathway.
SubsetPathwayData       Subset Pathway-Specific Data
SuperPCA_pVals          Test pathways with Supervised PCA
TransposeAssay          Transpose an Assay (Data Frame)
WhichPathways           Filter and Subset a 'pathwayCollection'-class
                        Object by Symbol.
wikipwsHS_Entrez_pathwayCollection
                        Wikipathways Homosapiens EntrezIDs
wikipwsHS_Symbol_pathwayCollection
                        Wikipathways Homosapiens Gene Symbols
write_gmt               Write a 'pathwayCollection' Object to a '.gmt'
                        File
