importFimoBindingSites: Prepare binding site by fimo results

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

Prepare binding site by fimo results

Description

Prepare binding sites by given fimo gff files

Usage

importFimoBindingSites(
  fimoGFFfiles,
  maximalBindingWidth = 40L,
  mergeBindingSitesByPercentage = 0.8,
  ignore.strand = TRUE,
  ...
)

Arguments

fimoGFFfiles	Filenames of gff files of fimo output.
maximalBindingWidth	A numeric vector(length=1). Maximal binding site width. Default is 40.
mergeBindingSitesByPercentage	A numeric vector (length=1). The percentage of overlapping region of binding sites to merge as one binding site.
ignore.strand	When set to TRUE, the strand information is ignored in the calculations.
...	Parameter to be passed to import.gff

Value

A GenomicRanges with all the positions of matches.

Author(s)

Jianhong Ou

Examples

extdata <- system.file('extdata', package='ATACseqTFEA')
fimoGFFfiles <- dir(extdata, 'fimo.*.gff', full.names=TRUE)
mts <- importFimoBindingSites(fimoGFFfiles)

jianhong/ATACseqTFEA documentation built on Feb. 9, 2024, 4:09 a.m.