expandBindingSites: Prepare the genomic ranges for proximal and distal regions...

In jianhong/ATACseqTFEA: Transcription Factor Enrichment Analysis for ATAC-seq

Prepare the genomic ranges for proximal and distal regions for counting

Description

Create multiple GRanges objects for downstream counting. The GRanges objects including bindingSitesWithGap: bindingSites with gaps and in both ends, bindingSitesWithProximal: bindingSites with gaps and proximal region in both ends, bindingSitesWithProximalAndGap: bindingSites with gaps, and then proximal and gaps in both ends, and bindingSitesWithDistal: bindingSites with gaps, proximal, gaps and distal regions.

Usage

expandBindingSites(bindingSites, proximal = 40L, distal = proximal, gap = 10L)

Arguments

bindingSites	A object of GenomicRanges indicates candidate binding sites. The prepareBindingSites function is a helper function to generate the binding sites. Users can also use other software for example fimo to generate the list.
proximal, distal	numeric(1) or integer(1). bases for open region from binding sites (proximal) and extended region for background (distal) of the binding region for aggregate ATAC-seq footprint.
gap	numeric(1) or integer(1). bases for gaps among binding sites, proximal, and distal. default is 10L.

Value

an GRangesList object with elements bindingSitesWithGap, bindingSitesWithProximal, bindingSitesWithProximalAndGap, and bindingSitesWithDistal for count5ends

Author(s)

Jianhong Ou

Examples

bsl <- system.file("extdata", "bindingSites.rds",
                   package="ATACseqTFEA")
bindingSites <- readRDS(bsl)
bs <- expandBindingSites(bindingSites)
length(bs)
names(bs)
lengths(bs)

jianhong/ATACseqTFEA documentation built on June 9, 2025, 1:39 a.m.