enrichmentTest {ClueR}

Fisher's exact test-based enrichment test

Description

Takes a vector of names representing phosphorylation sites that are partitioned in the same cluster and an kinase-substrate annotation. Test for enrichment of the kinase based on the name vector.

Usage

enrichmentTest(clust, annotation, universe, alter = "greater")

Arguments

clust

a vector of names representing phosphorylation sites that are partitioned in the same cluster

annotation

a list with names correspond to kinases and elements correspond to substrates belong to each kinase

universe

the universe of names to compare against

alter

indicates the alternative hypothesis and must be one of "two.sided", "greater" or "less"

Value

a matrix that contains enrichment of each kinase based on the input name vector.