GR2tfbs_db: Makes a TFBS-gene binding database

In TFEA.ChIP: Analyze Transcription Factor Enrichment

Description

GR2tfbs_db generates a TFBS-gene binding database through the association of ChIP-Seq peak coordinates (provided as a GenomicRange object) to overlapping genes or gene-associated Dnase regions (Ref.db).

Usage

GR2tfbs_db(Ref.db, gr.list, distanceMargin = 10,
  outputAsVector = FALSE)

Arguments

Ref.db	GenomicRanges object containing a database of reference elements (either Genes or gene-associate Dnase regions) including a gene_id metacolumn
gr.list	List of GR objects containing ChIP-seq peak coordinates (output of txt2GR).
distanceMargin	Maximum distance allowed between a gene or DHS to assign a gene to a ChIP-seq peak. Set to 10 bases by default.
outputAsVector	when 'TRUE', the output is a list of vectors instrad of a list of GeneSet objects

Value

List of GeneSe objetcs or vectors, one for every ChIP-Seq, storing the IDs of the genes to which the TF bound in the ChIP-Seq.

Examples

data('DnaseHS_db','gr.list', package='TFEA.ChIP')
GR2tfbs_db(DnaseHS_db, gr.list)

TFEA.ChIP documentation built on Nov. 8, 2020, 5:05 p.m.