gm_filter: gm_filter: GSEAmining GSEA output filter

In GSEAmining: Make Biological Sense of Gene Set Enrichment Analysis Outputs

Description

Filters a data frame containing the results of GSEA analysis.

Usage

gm_filter(df, p.adj = 0.05, neg_NES = 1, pos_NES = 1)

Arguments

df	Data frame that contains at least three columns: an ID column for the gene set names, a NES column with the normalized enrichment score and a core_enrichment column containing the genes in the leading edge of each gene set separated by '/'.
p.adj	An integer to set the limit of the adjusted p-value (or false discovery rate, FDR). Default value is 0.05
neg_NES	A positive integer to set the limit of negative NES. Default is 1.
pos_NES	A positive integer to set the limit of positive NES. Default is 1.

Value

A data frame.

Examples

data(genesets_sel)
gs.filt <- gm_filter(genesets_sel, p.adj = 0.05, neg_NES = 2.6, pos_NES = 2)

GSEAmining documentation built on Nov. 8, 2020, 5:52 p.m.