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