process_candidate_sites: Obtains and filters candidate sites from FIMO result

In HarteminkLab/TOP: Predict transcription factor occupancy using DNase- or ATAC-seq data

Obtains and filters candidate sites from FIMO result

Description

Gets candidate sites from FIMO motif matches and add flanking regions, and filters the candidate sites by different thresholds, and filters out sites in blacklist regions.

Usage

process_candidate_sites(
  fimo_file,
  flank = 100,
  thresh_pValue = 1e-05,
  thresh_pwmscore = 0,
  chr_order = paste0("chr", c(1:22, "X", "Y", "M")),
  blacklist_file = NULL,
  mapability_file = NULL,
  thresh_mapability = 0.8,
  bigWigAverageOverBed_path = "bigWigAverageOverBed"
)

Arguments

fimo_file	FIMO result ‘.txt’ file
flank	Flanking region (bp) around motif matches (default: 100)
thresh_pValue	FIMO p-value threshold (default: 1e-5)
thresh_pwmscore	FIMO PWM score threshold (default: 0)
chr_order	Chromosomes to include (default: 'chr1', ..., 'chr22', 'chrX', 'chrY', 'chrM'). Please change this accordingly if you use non-human data.
blacklist_file	Filename of the blacklist regions (default: NULL)
mapability_file	Filename of the mapability reference file
thresh_mapability	Mapability threshold (default: 0.8, candidate sites need to be mapable at least 80% positions). This is only used when the mapability_file is available.
bigWigAverageOverBed_path	Path to bigWigAverageOverBed executable (only needed when filtering mapability).

Value

A data frame of processed candidate binding sites passing the threshold filtering.

Examples

## Not run: 
sites <- process_candidate_sites(fimo_file='fimo.txt',
                                 thresh_pValue=1e-5,
                                 blacklist_file='blacklist.hg38.bed.gz')

## End(Not run)

HarteminkLab/TOP documentation built on July 27, 2023, 6:14 p.m.