pwmToCoverage: PWM hits and motif scores as an RLElist

In ThomasCarroll/soGGi: Visualise ChIP-seq, MNase-seq and motif occurrence as aggregate plots Summarised Over Grouped Genomic Intervals

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)

ThomasCarroll/soGGi documentation built on May 7, 2019, 8:40 a.m.