refinePWMMotifExtend {motifRG} | R Documentation |
Create an extended PWM model given a initial set of motif matches and input sequences
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, ...)
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 |
Flanking regions with length equal to flank is still included in output for reference
Same type of object returned by refinePWMMotif