pwmToCoverage {soGGi} | R Documentation

## PWM hits and motif scores as an RLElist

### Description

Creates rlelist of pwm hits.

Motif score as an RLElist

### Usage

    pwmToCoverage(pwm, genome, min = "70%", removeRand = FALSE,
      chrsOfInterest = NULL)

    makeMotifScoreRle(pwm, regions, genome, extend, removeRand = FALSE,
      strandScore = "mean", atCentre = FALSE)

### Arguments

`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.

### Value

A RLElist of motif density per base pair to be used as input to main soggi function.

### Author(s)

Thomas Carroll

### Examples

    data(pwmCov)
    data(singleGRange)

[Package soGGi version 1.12.0 Index]