SubsetPathwayCollection: Subset a 'pathwayCollection'-class Object by Pathway.

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

Subset a pathwayCollection-class Object by Pathway.

Description

The subset method for pathways lists as returned by the read_gmt function.

Usage

## S3 method for class 'pathwayCollection'
x[[name_char]]

Arguments

x	An object of class pathwayCollection.
name_char	The name of a pathway in the collection or its unique ID.

Details

This function finds the index matching the name_char argument to the TERMS field of the pathwayCollection-class Object, then subsets the pathways list, TERMS vector, description vector, and setsize vector by this index. If you subset a trimmed pathwayCollection object, and the function errors with "Pathway not found.", then the pathway specified has been trimmed from the pathway collection.

Also, this function does not allow for users to overwrite any portion of a pathway collection. These objects should rarely, if ever, be changed. If you absolutely must change the components of a pathwayCollection object, then create a new one with the codeCreatePathwayCollection function.

Value

A list of the pathway name (Term), unique ID (pathID), contents (IDs), description (description), and number of features (Size).

Examples

  data("colon_pathwayCollection")
  colon_pathwayCollection[["KEGG_RETINOL_METABOLISM"]]

gabrielodom/pathwayPCA documentation built on July 10, 2023, 3:32 a.m.