Obtains and filters candidate sites from FIMO result

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.

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

if (FALSE) {
sites <- process_candidate_sites(fimo_file='fimo.txt',
                                 thresh_pValue=1e-5,
                                 blacklist_file='blacklist.hg38.bed.gz')
}