fimo_motif_matches: Runs 'FIMO' to scan for motif matches

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

Runs FIMO to scan for motif matches

Description

Runs FIMO to scan for motif matches along the genome.

Usage

fimo_motif_matches(
  motif_file,
  sequence_file,
  outname = "fimo.txt",
  outdir = dirname(outname),
  thresh_pValue = 1e-05,
  background = c("default", "motif", "uniform", "file"),
  background_file,
  skip_matched_sequence = TRUE,
  max_strand = FALSE,
  max_stored_scores = 1e+05,
  options = "",
  verbosity = 2,
  fimo_path = "fimo"
)

Arguments

motif_file	Motif file in MEME format.
sequence_file	Genome sequence file in FASTA format.
outname	Output file name.
outdir	Output directory.
thresh_pValue	FIMO option thresh for p-value threshold.
background	Option for background model: ‘default’: uses FIMO default background setting; ‘motif’: uses the 0-order letter frequencies contained in the motif file; ‘uniform’: uses uniform letter frequencies; ‘file’: uses the file specified in background_file.
background_file	Path to a file in Markov Background Model Format.
skip_matched_sequence	FIMO option skip_matched_sequence. Turns off output of the sequence of motif matches. This speeds up processing considerably.
max_strand	FIMO option max_strand. If matches on both strands at a given position satisfy the output threshold, only report the match for the strand with the higher score. If the scores are tied, the matching strand is chosen at random.
max_stored_scores	The maximum number of stored matches.
options	Other options for FIMO.
verbosity	A number of the verbosity level (from 1 to 5). If set to 1 (quiet) then it will only output error messages, in contrast, the other extreme 5 (dump) outputs lots of mostly useless information.
fimo_path	Path to fimo command line executable. (default: 'fimo')

Examples

## Not run: 
fimo_motif_matches(motif_file='motifID.meme',
                   sequence_file='hg38.fa',
                   thresh_pValue=1e-5,
                   outname='motifID_1e-5.fimo.txt',
                   fimo_path='fimo')

## End(Not run)

HarteminkLab/TOP documentation built on June 11, 2025, 5:34 p.m.