Function reference • pathwayPCA

Pathway Collections Functions to create or modify pathway collection objects
`read_gmt()`	Read a `.gmt` file in as a `pathwayCollection` object
`write_gmt()`	Write a `pathwayCollection` Object to a `.gmt` File
`CreatePathwayCollection()`	Manually Create a `pathwayCollection`-class Object.
`print(<pathwayCollection>)`	Display the Summary of a `pathwayCollection`-class Object.
`[[`(<pathwayCollection>)	Subset a `pathwayCollection`-class Object by Pathway.
Creating S4-Class Objects and Basic Methods Descriptions, creators, and accessors of the Omics* S4 classes
`OmicsPathway-class`	An S4 class for mass spectrometry or bio-assay data and gene pathway lists
`OmicsSurv-class`	An S4 class for survival responses within an `OmicsPathway` object
`OmicsReg-class`	An S4 class for continuous responses within an `OmicsPathway` object
`OmicsCateg-class`	An S4 class for categorical responses within an `OmicsPathway` object
`ValidOmicsSurv()` `ValidOmicsReg()` `ValidOmicsCateg()`	Check validity of new Omics*-class objects
`TransposeAssay()`	Transpose an Assay (Data Frame)
`SE2Tidy()`	Tidy a SummarizedExperiment Assay
`CreateOmics()`	Generation Wrapper function for `-Omics*`-class objects
`show(<OmicsPathway>)`	Display the Summary of an `Omics*`-class Object.
`getAssay()` `getAssay<-`() `getSampleIDs()` `getSampleIDs<-`() `getPathwayCollection()` `getPathwayCollection<-`() `getTrimPathwayCollection()`	Access and Edit Assay or `pathwayCollection` Values in `Omics*` Objects
`getEventTime()` `getEventTime<-`() `getEvent()` `getEvent<-`()	Access and Edit Event Time or Indicator in an `OmicsSurv` Object
`getResponse()` `getResponse<-`()	Access and Edit Response of an `OmicsReg` or `OmicsReg` Object
PCA-method Functions Functions to analyze Omics-class objects
`aespca()`	Adaptive, elastic-net, sparse principal component analysis
`AESPCA_pVals()`	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
`CreateOmicsPath()` `CreateOmicsSurv()` `CreateOmicsReg()` `CreateOmicsCateg()`	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.
`getAssay()` `getAssay<-`() `getSampleIDs()` `getSampleIDs<-`() `getPathwayCollection()` `getPathwayCollection<-`() `getTrimPathwayCollection()`	Access and Edit Assay or `pathwayCollection` Values in `Omics*` Objects
`getResponse()` `getResponse<-`()	Access and Edit Response of an `OmicsReg` or `OmicsReg` Object
`getEventTime()` `getEventTime<-`() `getEvent()` `getEvent<-`()	Access and Edit Event Time or Indicator in an `OmicsSurv` 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
`[[`(<pathwayCollection>)	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
Example Data Sets Data for function examples
`colon_pathwayCollection`	Gene Pathway Subset
`colonSurv_df`	Colon Cancer -Omics Data
`wikipwsHS_Entrez_pathwayCollection`	Wikipathways Homosapiens EntrezIDs
Internal AES-PCA Functions Functions designed to be called by the AES-PCA wrapper above
`aespca()`	Adaptive, elastic-net, sparse principal component analysis
`lars.lsa()`	Least Angle Regression and LASSO Regression
`ExtractAESPCs()`	Extract AES-PCs from recorded pathway-subsets of a mass spectrometry or bio-assay data frame
`PermTestSurv()`	AES-PCA permutation test of survival response for pathway PCs
`PermTestReg()`	AES-PCA permutation test of continuous response for pathway PCs
`PermTestCateg()`	AES-PCA permutation test of categorical response for pathway PCs
`normalize()`	Normalize and reconstruct the eigenvalues of a data matrix for supervised PCA
Internal Supervised PCA Functions Functions designed to be called by the Supervised PCA wrapper above
`coxTrain_fun()`	Train Cox Proportional Hazards model for supervised PCA
`olsTrain_fun()`	Gene-specific Regularized Ordinary Least Squares fit statistics for supervised PCA
`glmTrain_fun()`	Gene-specific Generalized Linear Model fit statistics for supervised PCA
`superpc.st()`	Extract and test principal components from supervised PCA
`superpc.train()`	Train a supervised PCA model
`mysvd()`	Singular Value Decomposition wrapper for supervised PCA
`OptimGumbelMixParams()`	Calculate the optimal parameters for a mixture of Weibull Extreme Value Distributions for supervised PCA
`GumbelMixpValues()`	Calculate the \(p\)-values from an optimal mixture of Weibull Extreme Value distributions for supervised PCA
`pathway_tControl()`	Calculate pathway-specific Student's \(t\)-scores from a null distribution for supervised PCA
`pathway_tScores()`	Calculate pathway-specific Student's \(t\)-scores for supervised PCA
Internal Supplemental Functions Utility functions shared by both the AES-PCA and supervised PCA methods or CreateOmics
`CreateOmicsPath()` `CreateOmicsSurv()` `CreateOmicsReg()` `CreateOmicsCateg()`	Generation functions for `-Omics*`-class objects
`IntersectOmicsPwyCollct()`	Delete -Ome symbols or IDs without matching features recorded in a given assay data frame from a pathway collection
`TabulatepValues()`	Tabulate, adjust, and sort pathway \(p\)-values
`ControlFDR()`	Adjust \(p\)-values for simple multiple-testing procedures
`SampleResponses()` `SampleSurv()` `SampleReg()` `SampleCateg()`	Parametric bootstrap and non-parametric permutations of a response vector or matrix

Reference

Pathway Collections

Creating S4-Class Objects and Basic Methods

PCA-method Functions

Example Data Sets

Internal AES-PCA Functions

Internal Supervised PCA Functions

Internal Supplemental Functions

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