SubsetPathwayData: Subset Pathway-Specific Data

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

Description

Given an Omics object and the name of a pathway, return the -omes in the assay and the response as a (tibble) data frame.

Usage

SubsetPathwayData(object, pathName, ...)

## S4 method for signature 'OmicsPathway'
SubsetPathwayData(object, pathName, ...)

Arguments

object	An object of class OmicsPathway, or an object extending this class.
pathName	The name of a pathway contained in the pathway collection in the object.
...	Dots for additional internal arguments (currently unused).

Details

This function subsets the assay by the matching gene symbols or IDs in the specified pathway.

Value

A data frame of the columns of the assay in the Omics object which are listed in the specified pathway, with a leading column for sample IDs. If the Omics object has response information, these are also included as the first column(s) of the data frame, after the sample IDs. If you have the suggested tidyverse package suite loaded, then this data frame will print as a tibble. Otherwise, it will print as a data frame.

Examples

  data("colonSurv_df")
  data("colon_pathwayCollection")

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

  SubsetPathwayData(
    colon_Omics,
    "KEGG_RETINOL_METABOLISM"
  )

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