score_geneset_oddsratio: Compute odds-ratio for each geneset

In goat: Gene Set Analysis Using the Gene Set Ordinal Association Test

Compute odds-ratio for each geneset

Description

gs_signif = number of significant genes in geneset G that intersect with user's genelist (i.e. foreground genes in G) gs_all = number of genes in geneset G that intersect with user's genelist (i.e. foreground+background genes in G) k_signif = total number of significant genes in user's genelist k_all = total number of genes in user's genelist

gs_signif/gs_all = ratio of foreground genes in geneset G k_signif/k_all = ratio of overall foreground genes (i.e. expected value for a random geneset)

oddsratio = (gs_signif/gs_all) / (k_signif/k_all)

Usage

score_geneset_oddsratio(genesets, genelist)

Arguments

genesets	tibble with genesets, must contain columns 'source', 'id', 'ngenes', 'ngenes_signif'
genelist	tibble with genes, must contain columns 'gene', 'signif'

Value

input genesets with results in column "score_oddsratio"

goat documentation built on April 3, 2025, 6:05 p.m.