hypergeometric {ActivePathways}

Hypergeometric test

Description

Perform a hypergeometric test, also known as the Fisher's exact test, on a 2x2 contingency table with the alternative hypothesis set to 'greater'. In this application, the test finds the probability that counts[1, 1] or more genes would be found to be annotated to a term (pathway), assuming the null hypothesis of genes being distributed randomly to terms.

Usage

hypergeometric(counts)

Arguments

counts

A 2x2 numerical matrix representing a contingency table.

Value

a p-value of enrichment of genes in a term or pathway.