# Integrative Pathway Analysis with Modern PCA Methodology and Gene Selection

## Documentation for package ‘pathwayPCA’ version 1.16.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

aespca | Adaptive, elastic-net, sparse principal component analysis
AESPCA_pVals | Test pathway association with AES-PCA
AESPCA_pVals-method | Test pathway association with AES-PCA
colonSurv_df | Colon Cancer -Omics Data
colon_pathwayCollection | Gene Pathway Subset
Contains | Check if a long atomic vector contains a short atomic vector
CreateOmics | Generation Wrapper function for '-Omics*'-class objects
CreateOmicsCateg | Generation functions for '-Omics*'-class objects
CreateOmicsPath | Generation functions for '-Omics*'-class objects
CreateOmicsReg | Generation functions for '-Omics*'-class objects
CreateOmicsSurv | Generation functions for '-Omics*'-class objects
CreatePathwayCollection | Manually Create a 'pathwayCollection'-class Object.
getAssay | Access and Edit Assay or 'pathwayCollection' Values in 'Omics*' Objects
getAssay-method | Access and Edit Assay or 'pathwayCollection' Values in 'Omics*' Objects
getAssay<- | Access and Edit Assay or 'pathwayCollection' Values in 'Omics*' Objects
getAssay<--method | Access and Edit Assay or 'pathwayCollection' Values in 'Omics*' Objects
getEvent | Access and Edit Event Time or Indicator in an 'OmicsSurv' Object
getEvent-method | Access and Edit Event Time or Indicator in an 'OmicsSurv' Object
getEvent<- | Access and Edit Event Time or Indicator in an 'OmicsSurv' Object
getEvent<--method | Access and Edit Event Time or Indicator in an 'OmicsSurv' Object
getEventTime | Access and Edit Event Time or Indicator in an 'OmicsSurv' Object
getEventTime-method | Access and Edit Event Time or Indicator in an 'OmicsSurv' Object
getEventTime<- | Access and Edit Event Time or Indicator in an 'OmicsSurv' Object
getEventTime<--method | Access and Edit Event Time or Indicator in an 'OmicsSurv' Object
getPathPCLs | Extract PCs and Loadings from a 'superpcOut'- or 'aespcOut'-class Object.
getPathPCLs.aespcOut | Extract PCs and Loadings from a 'superpcOut'- or 'aespcOut'-class Object.
getPathPCLs.superpcOut | Extract PCs and Loadings from a 'superpcOut'- or 'aespcOut'-class Object.
getPathpVals | Extract Table of p-values from a 'superpcOut'- or 'aespcOut'- class Object.
getPathpVals.aespcOut | Extract Table of p-values from a 'superpcOut'- or 'aespcOut'- class Object.
getPathpVals.superpcOut | Extract Table of p-values from a 'superpcOut'- or 'aespcOut'- class Object.
getPathwayCollection | Access and Edit Assay or 'pathwayCollection' Values in 'Omics*' Objects
getPathwayCollection-method | Access and Edit Assay or 'pathwayCollection' Values in 'Omics*' Objects
getPathwayCollection<- | Access and Edit Assay or 'pathwayCollection' Values in 'Omics*' Objects
getPathwayCollection<--method | Access and Edit Assay or 'pathwayCollection' Values in 'Omics*' Objects
getResponse | Access and Edit Response of an 'OmicsReg' or 'OmicsReg' Object
getResponse-method | Access and Edit Response of an 'OmicsReg' or 'OmicsReg' Object
getResponse<- | Access and Edit Response of an 'OmicsReg' or 'OmicsReg' Object
getResponse<--method | Access and Edit Response of an 'OmicsReg' or 'OmicsReg' Object
getSampleIDs | Access and Edit Assay or 'pathwayCollection' Values in 'Omics*' Objects
getSampleIDs-method | Access and Edit Assay or 'pathwayCollection' Values in 'Omics*' Objects
getSampleIDs<- | Access and Edit Assay or 'pathwayCollection' Values in 'Omics*' Objects
getSampleIDs<--method | Access and Edit Assay or 'pathwayCollection' Values in 'Omics*' Objects
getTrimPathwayCollection | Access and Edit Assay or 'pathwayCollection' Values in 'Omics*' Objects
getTrimPathwayCollection-method | Access and Edit Assay or 'pathwayCollection' Values in 'Omics*' Objects
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
SubsetPathwayData-method | Subset Pathway-Specific Data
SuperPCA_pVals | Test pathways with Supervised PCA
SuperPCA_pVals-method | 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
[[.pathwayCollection | Subset a 'pathwayCollection'-class Object by Pathway.