refinePWMMotifExtend: create an extended PWM (Position Weight Model) model given a...

In motifRG: A package for discriminative motif discovery, designed for high throughput sequencing dataset

Description

Create an extended PWM model given a initial set of motif matches and input sequences

Usage

  refinePWMMotifExtend(motifs=NULL, seqs, pwm.ld=NULL, flank=3,  extend.tol=10^-3, trim.rel.entropy=0.2,  null=rep(0.25, 4), max.width=20, ...)

Arguments

motifs	The initial set of motif matches. character vector or DNAStringSet object
seqs	Input sequences. character vector or DNAStringSet object
pwm.ld	The initial PWM matrixes in logodds transformation. Either "motifs" or "pwm.ld" is not NULL
flank	The number of bases for extension on both sides of the motif. The extension will be iterated if the there is sufficient signal in the flanking region.
extend.tol	Convergence criteria for extension.
trim.rel.entropy	cutoff to be used to trim the uninformative flanking of a PWM model based on relative entropy against a null distribution.
null	NULL background distribution
max.width	The maximum width of PWM
...	other arguments passed to function refinePWMMotif

Details

Flanking regions with length equal to flank is still included in output for reference

Value

Same type of object returned by refinePWMMotif

See Also

findMotif refinePWMMotif

motifRG documentation built on April 28, 2020, 8:46 p.m.