GR2tfbs_db {TFEA.ChIP} | R Documentation

## Makes a TFBS-gene binding database

### 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)

[Package TFEA.ChIP version 1.12.0 Index]