pwmDistance: pwmDistance

In chromVAR: Chromatin Variation Across Regions

Description

computes distance between every pwm in a list or between pwms in one list with pwms in another

Usage

pwmDistance(x, y = NULL, min_overlap = 5)

Arguments

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

Details

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.

Value

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.

Examples

motifs <- getJasparMotifs()
library(TFBSTools)
pwm_dists <- pwmDistance(toPWM(motifs[[1]]), toPWM(motifs[[2]]))

chromVAR documentation built on Nov. 8, 2020, 6:46 p.m.