pwmToCoverage {soGGi} | R Documentation |
Creates rlelist of pwm hits.
Motif score as an RLElist
pwmToCoverage(pwm, genome, min = "70%", removeRand = FALSE, chrsOfInterest = NULL) makeMotifScoreRle(pwm, regions, genome, extend, removeRand = FALSE, strandScore = "mean", atCentre = FALSE)
pwm |
A PWM matrix object. |
genome |
A BSgenome object |
min |
pwm score (as percentage of maximum score) cutoff |
removeRand |
Remove contigs with rand string |
chrsOfInterest |
Chromosomes to use |
regions |
GRanges object to include in pwm rlelist |
extend |
bps to extend regions by |
strandScore |
Method for averaging strand. Options are max, mean, sum, bothstrands |
atCentre |
TRUE/FALSE. TRUE assigns score onto 1bp position at centre of motif. FALSE assigns every basepair the sum of scores of all overlapping motifs. |
A RLElist of motif density per base pair to be used as input to main soggi function.
Thomas Carroll
data(pwmCov) data(singleGRange)