getPathPCLs: Extract PCs and Loadings from a 'superpcOut'- or...

In pathwayPCA: Integrative Pathway Analysis with Modern PCA Methodology and Gene Selection

Description

Given an object of class aespcOut or superpcOut, as returned by the functions AESPCA_pVals or SuperPCA_pVals, respectively, and the name or unique ID of a pathway, return a data frame of the principal components and a data frame of the loading vectors corresponding to that pathway.

Usage

getPathPCLs(pcOut, pathway_char, ...)

## S3 method for class 'superpcOut'
getPathPCLs(pcOut, pathway_char, ...)

## S3 method for class 'aespcOut'
getPathPCLs(pcOut, pathway_char, ...)

Arguments

pcOut	An object of classes superpcOut or aespcOut as returned by the SuperPCA_pVals or AESPCA_pVals functions, respectively.
pathway_char	A character string of the name or unique identifier of a pathway
...	Dots for additional arguments (currently unused).

Details

Match the supplied pathway character string to either the pathways or terms columns of the pVals_df data frame within the pcOut object. Then, subset the loadings_ls and PCs_ls lists for their entries which match the supplied pathway. Finally, return a list of the PCs, loadings, and the pathway ID and name.

Value

A list of four elements:

• PCs : A data frame of the principal components

• Loadings : A matrix of the loading vectors with features in the row names

• pathway : The unique pathway identifier for the pcOut object

• term : The name of the pathway

NULL

NULL

Examples

  ###  Load Data  ###
  data("colonSurv_df")
  data("colon_pathwayCollection")

  ###  Create -Omics Container  ###
  colon_Omics <- CreateOmics(
    assayData_df = colonSurv_df[, -(2:3)],
    pathwayCollection_ls = colon_pathwayCollection,
    response = colonSurv_df[, 1:3],
    respType = "survival"
  )

  ###  Calculate Supervised PCA Pathway p-Values  ###
  colon_superpc <- SuperPCA_pVals(
    colon_Omics,
    numPCs = 2,
    parallel = TRUE,
    numCores = 2,
    adjustment = "BH"
  )

  ###  Extract PCs and Loadings  ###
  getPathPCLs(
    colon_superpc,
    "KEGG_PENTOSE_PHOSPHATE_PATHWAY"
  )

pathwayPCA documentation built on Dec. 15, 2020, 6:14 p.m.