prepareBindingSites: Prepare binding site for TFEA

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

Prepare binding site for TFEA

Description

Prepare binding sites by given position weight matrix and genome.

Usage

prepareBindingSites(
  pwms,
  genome,
  seqlev = seqlevels(genome),
  p.cutoff = 1e-05,
  w = 7,
  grange,
  maximalBindingWidth = 40L,
  mergeBindingSitesByPercentage = 0.8,
  ignore.strand = TRUE
)

Arguments

pwms	either PFMatrix, PFMatrixList, PWMatrix, PWMatrixList
genome	BSgenome object.
seqlev	A character vector. Sequence levels to be searched.
p.cutoff	p-value cutoff for returning motifs; default is 1e-05
w	parameter controlling size of window for filtration; default is 7
grange	GRanges for motif search. If it is set, function will only search the binding site within the grange. Usually a peak list should be supplied.
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.

Value

A GenomicRanges with all the positions of matches.

Author(s)

Jianhong Ou

Examples

library(TFBSTools)
motifs <- readRDS(system.file("extdata", "PWMatrixList.rds",
                              package="ATACseqTFEA"))
library(BSgenome.Drerio.UCSC.danRer10)
seqlev <- "chr1" #paste0("chr", 1:25)
mts <- prepareBindingSites(motifs, Drerio, seqlev,
                           grange=GRanges("chr1",
                                          IRanges(5000, 100000)))

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