test_genesets_hypergeometric: Geneset ORA using hypergeometric test

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

Geneset ORA using hypergeometric test

Description

In most cases, it's more convenient to call the more generic test_genesets function which also deals with multiple-testing correction (per geneset source)

It is assumed that the genesets and genelist parameters are in sync, i.e. genesets provided here is the result of the filter_genesets() function (using the same genelist table)

Only genesets with at least 1 significant gene are subjected to statistical testing (e.g. NA is returned for genesets without significant genes)

Usage

test_genesets_hypergeometric(genesets, genelist, require_nsignif = 1L)

Arguments

genesets	tibble with genesets, must contain columns 'id', 'ngenes' and 'ngenes_signif'
genelist	tibble with genes, must contain column 'signif'. The number of rows in this table (where signif is not NA) is assumed to be the total number of tested genes, the number of rows where signif==TRUE is assumed the total number of significant genes.
require_nsignif	minimum number of 'signif genes' that overlap with a geneset; NA pvalues are returned for genesets with ngenes_signif <= require_nsignif. This function 'prefilters' genesets, so beware that this will influence downstream multiple testing correction. Default is 1

Value

input genesets table with results in the "pvalue" column

See Also

test_genesets

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