getMotifEnrichment-DsATAC-method: getMotifEnrichment-methods

In demuellae/ChrAccR: Analyzing chromatin accessibility data in R

Description

Perform enrichment analysis for (TF) motifs of a query set of regions. Fisher's Exact Test is employed to test the association of motif present in the query set against the background of all regions of that type covered in the object

Usage

## S4 method for signature 'DsATAC'
getMotifEnrichment(.object, type, idx, motifs = "jaspar")

Arguments

.object	DsATAC object
type	character string specifying the region type
idx	logical vector or indices of the same length as length(getCoord(.object)) specifies the query set
motifs	either a character string (currently only "jaspar" and sets contained in chromVARmotifs ("homer", "encode", "cisbp") are supported) or an object containing PWMs that can be used by motifmatchr::matchMotifs (such as an PFMatrixList or PWMatrixList object)

Value

a data.frame summarizing Fisher's Exact Test enrichment statistics for each motif

Author(s)

Fabian Mueller

demuellae/ChrAccR documentation built on Jan. 20, 2020, 3:03 a.m.