find_motifs(fasta,
minw = 8,
maxw = 20,
nmotifs = -1,
noccurs = 12,
seedingCutoff = 0.65,
scanMinW = 6,
scanCutoff = 0.8,
cleanMotif = 0.5,
significant.sites = 4,
seeds = NULL,
debug = FALSE);
fasta
a fasta sequence collection for make the motif discovery, which should contains multiple sequence.
minw%
the minimum motif width in chars.
maxw%
the maximum motif width in chars.
nmotifs
A number for limit the number of motif outputs:
- negative integer/zero: no limits[default]
- positive value: top motifs with score desc
. [as integer]
noccurs%
the minimum occurrence number of the motif sites in the input sequence collection for keep a motif.
seedingCutoff
the similarity cutoff threshold value for build the seed clusters. [as double]
scanMinW
the minimum width of the seed scan region. [as integer]
scanCutoff
the similarity score cutoff threshold value of the seed scan. [as double]
cleanMotif
the motif cleaning threshold value for remove the low score motif sites from the generated motif model. [as double]
significant.sites
the minimum number of the significant sites for keep a seed. [as integer]
seeds
the pre-computed seed data for make the motifs, which can be a ScanFile object that is created by the create.seeds api, or a collection of the HSP seed object. If this parameter is not specified, then the seeds will be discovered from the input sequence data automatically.
debug
print the debug log message of the motif discovery progress?. [as boolean]
env
the R# runtime environment object. [as Environment]