refinePWMMotifExtend {motifRG} | R Documentation

## create an extended PWM (Position Weight Model) model given a initial set of motif matches and input sequences

### 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`

[Package motifRG version 1.30.0 Index]