computePairwiseEnrichments: Pairwise motif enrichment analysis across a database of...

In jsalojar/TFbindR: Identification and Counting of the Occurence of Motifs in a Set of Promoter Sequences. Motif Enrichment Analysis

Description

Test for pairwise motif enrichment in a set of genes of interest. The function performs a fisher exact test to calculte the enrichment of each motif combination for the set of selected genes, from the background genes in promoter.DB.

Usage

computeEnrichments(Genes, promoterDB = "promoter.DB")

Arguments

Genes	list of the genes of interest
promoterDB	promoterDB object

Value

An R object with 3 elements. Each of the elements is a data frame with motif combination on the rows and the enrichment statistics on the columns. Each row corresponds to one-sided fisher.test for enirchment of a motif pair in the given gene set, based on combined occurence of the motifs in the plus, minus or both strands combined. The columns of the data frame are:

p.value - the p.value of the Fisher test,

odds.ratio - the estimate of the odds ration from the Fisher test,

genes - subset of the genes that are enirched with the motif and

p.adj.BH - the multiple test correction of the p.value with the "BH" adjustment.

Examples

# Read an example gene set. 
genes=read.table(system.file("extdata","test_geneSet.txt",package="TFbindR"),stringsAsFactors=F)

# Run the function with the promoterDB generated by the function makePromoterDBfromFIMO.
pairwise_enrichment=computePairwiseEnrichments(as.character(unlist(genes)), "TAIR10_500bp_upstream.fimo.db.rda") 

jsalojar/TFbindR documentation built on Dec. 9, 2019, 12:16 a.m.