pwmDistance {chromVAR} | R Documentation

## pwmDistance

### 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]]))

[Package chromVAR version 1.8.0 Index]