makeChIPGeneDB: Make a ChIP - target database

In LauraPS1/TFEA.ChIP: Analyze Transcription Factor Enrichment

Make a ChIP - target database

Description

makeChIPGeneDB generates a ChIP-seq - target database through the association of ChIP-Seq peak coordinates (provided as a GenomicRange object) to overlapping genes or gene-associated genomic regions (Ref.db).

Usage

makeChIPGeneDB(Ref.db, gr.list, distanceMargin = 10, min.Targets = 10)

Arguments

Ref.db	GenomicRanges object containing a database of reference elements (either Genes or gene-associated 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 regulatory element to assign a gene to a ChIP-seq peak. Set to 10 bases by default.
min.Targets	Minimum number of putative targets per ChIP-seq in gr.list. ChIPs with fewer targets will be discarded. regulatory element to assign a gene to a ChIP-seq peak. Set to 10 bases by default.

Value

List containing two elements: - Gene Keys: vector of gene IDs - ChIP Targets: list of vectors, one per element in gr.list, containing the putative targets assigned. Each target is coded as its position in the vector 'Gene Keys'.

Examples

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

LauraPS1/TFEA.ChIP documentation built on April 21, 2023, 7:29 a.m.