computes distance between every pwm in a list or between pwms in one list with pwms in another
pwmDistance(x, y = NULL, min_overlap = 5)
| x | list of pwms or pfms, see Details |
|---|---|
| y | list of pwms or pfms, see Details |
| min_overlap | minimum number of basepairs overlapping between motifs |
a list with three matrices- 'dist' has the distance between each pair of motifs, 'strand' has the strand of the motif for the match, and 'offset' has the offset between the motifs.
The format of x and y should be a
PWMatrixList
or PFMatrixList or a list of matrices with rows
corresponding to "A","C","G","T" and columns summing to 1.
# NOT RUN { motifs <- getJasparMotifs() library(TFBSTools) pwm_dists <- pwmDistance(toPWM(motifs[[1]]), toPWM(motifs[[2]])) # }