find_motifs {bioseq.patterns} R Documentation

find possible motifs of the given sequence collection

Description

Usage

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);

Arguments

fasta

should contains multiple sequence

minw%

-

maxw%

-

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%

-

Details

Authors

seqtoolkit

Value

this function returns data object of type SequenceMotif.

clr value class

Examples

[Package bioseq.patterns version 1.0.0.0 Index]