Runs FIMO to scan for motif matches along the genome.
fimo_motif_matches(
motif_file,
sequence_file,
outname = "fimo.txt",
outdir = dirname(outname),
thresh_pValue = 1e-04,
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"
)Motif file in MEME format.
Genome sequence file in FASTA format.
Output file name.
Output directory.
FIMO option thresh for p-value threshold.
Option for background model:
‘default’: use FIMO default background setting;
‘motif’: use the 0-order letter frequencies contained in the motif file;
‘uniform’: use uniform letter frequencies;
‘file’: use the file specified in background_file.
Path to a file in Markov Background Model Format.
FIMO option skip_matched_sequence.
Turns off output of the sequence of motif matches.
This speeds up processing considerably.
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.
The maximum number of stored matches.
Other options for FIMO.
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.
Path to fimo command line executable.
if (FALSE) {
fimo_motif_matches(motif_file='motifID.meme',
sequence_file='hg38.fa',
thresh_pValue=1e-5,
outname='motifID_1e-5.fimo.txt',
fimo_path='fimo')
}