PWM hits and motif scores as an RLElist

Description

Creates rlelist of pwm hits.

Motif score as an RLElist

Usage

1
2
3
4
5
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

1
2