termEnrichment: termEnrichment

In Distue/termEnrichment: Easy enrichment testing for multiple terms over a background

Description

This function calculates enrichment for a set of features against a set of background features.

Usage

termEnrichment(termTable, foregroundIDs, universeIDs, annotation, terms, padj.cutoff, padj.method, alternative, parallel, removeDuplicatedTerms)

Arguments

termTable	data.frame or tibble ID where first column is an ID column and the second column are associated terms to be tested against
foregroundIDs	vector of IDs defining the foreground (must be same IDs as is first column of termTable)
universeIDs	vector of IDs defining the universe (must be same IDs as is first column of termTable)
annotation	data.frame or tibble annotating terms (first column must be term identifier)
terms	specifies what terms will be tested for. tests all existing terms if NULL
permutations	number of permutations used for caluclating mean background ranks for random samples data
correction	logical. TRUE if p-value correction is applied
padj.cutoff	cutoff for p.adjusted value
padj.method	p adjustment method, default is "ihw" see ?ihw, other options are "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none" from ?p.adjust
alternative	alternative hypothesis for fisher exact test, see ?fisher.test
parallel	logical the testing be parallised with BiocParallel
quiet	non verbose output
removeDuplicatedTerms	removes duplicated terms in termTable if necessary
...	parameter list forwarded to fisher.test functions

Value

tibble annotated analysis results

Author(s)

Thomas Schwarzl <[e-mail]>

Examples

data(yeastGO)
data(universeIDs)
data(foregroundIDs)
data(yeastGOdesc)

termEnrichment(yeastGO, foregroundIDs, universeIDs,
               annotation = yeastGOdesc)

Distue/termEnrichment documentation built on March 6, 2020, 9:28 a.m.