subsetEnrichedPathways: Subset enriched pathways of RAV

In shbrief/PCAGenomicSignatures: Interpretation of RNA-seq experiments through robust, efficient comparison to public databases

Subset enriched pathways of RAV

Description

Subset enriched pathways of RAV

Usage

subsetEnrichedPathways(
  RAVmodel,
  ind = NULL,
  n = 10,
  both = FALSE,
  include_nes = FALSE
)

Arguments

RAVmodel	PCAGenomicSignatures object. Also an output from GSEA can be used.
ind	A numeric vector containing the RAV number you want to check enriched pathways. If not specified, this function returns results from all the RAVs.
n	The number of top and bottom pathways to be selected based on normalized enrichment score (NES).
both	Default is FALSE, where only the top n pathways will be printed. If it is set to TRUE, the output will contain both top and bottom n pathways.
include_nes	Defalt is FALSE. If it set to TRUE, the output will include both description and NES of the enriched pathway.

Value

A DataFrame with top and bottom n pathways from the enrichment results.

Examples

data(miniRAVmodel)

# all RAVS in model
subsetEnrichedPathways(miniRAVmodel,n=5)

# only a specific RAV (note the colnames above)
subsetEnrichedPathways(miniRAVmodel,ind=695,n=5)

shbrief/PCAGenomicSignatures documentation built on May 3, 2023, 11:21 a.m.