GSEA.Analyze.Sets: Performs leading edge analysis of a GSEA result

In GSEA-MSigDB/GSEA_R: Gene Set Enrichment Analysis (GSEA)

Description

'GSEA.Analyze.Sets' returns leading edge plots and gcts extracted from a GSEA result folder

Usage

GSEA.Analyze.Sets(directory = getwd(), topgs = 20, height = 16,
  width = 16, gsea.type = "GSEA", doc.string = "gsea_result")

Arguments

directory	The directory containing GSEA result files
topgs	Number of gene sets from GSEA output used for leading edge analysis (default: 20)
height	height dimension for leading edge analysis plots
width	width dimension for leading edge analysis plots
gsea.type	the gsea run type (either 'GSEA' or 'preranked')
doc.string	the file prefixed in the original analysis (typically user defined)

Details

This function is designed to be invoked immediately after 'GSEA' to run leading edge analysis.

Value

Leading edge analysis plots and GCT files containing the leading edge subsets for each class

Examples

## Not run: GSEA.Analyze.Sets(doc.string = "gsea_result")

GSEA-MSigDB/GSEA_R documentation built on Nov. 30, 2021, 4:50 a.m.