SubsetPathwayData {pathwayPCA} | R Documentation

## Subset Pathway-Specific Data

### 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"
      )

[Package pathwayPCA version 1.0.0 Index]