Integrative Pathway Analysis with Modern PCA Methodology and Gene Selection


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Documentation for package ‘pathwayPCA’ version 1.22.0

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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.