make a motif scan from the given sequence collection

gibbs_scan {bioseq.patterns}

R Documentation

make a motif scan from the given sequence collection

Description

Usage

gibbs_scan(seqs,
    width = NULL,
    maxitr = 1000);

Arguments

seqs

a fasta sequence collection for run the gibbs sampler motif discovery, which can be a FastaFile object, a collection of the FastaSeq object, or a character vector of the raw sequence data.

width

the motif width of the gibbs sampler. If this parameter is not specified, then the motif width will be evaluated from the input sequence data automatically as the 60% of the average sequence length. [as integer]

maxitr

the maximum iteration number of the gibbs sampler. [as integer]

env

the R# runtime environment object. [as Environment]

Authors

seqtoolkit

Value

a MSAMotif motif object that discovered from the given sequence collection by the gibbs sampler;

this function returns NULL if the input sequence data can not be cast to a fasta sequence collection.

clr value class

MSAMotif

[Package bioseq.patterns version 1.0.0.0 Index]