makeMotifScoreRle

pwmToCoverage

genome

pwm score (as percentage of maximum score) cutoff

removeRand

chrsOfInterest

regions

extend

Method for averaging strand. Options are max, mean, sum, bothstrands

strandScore

TRUE/FALSE. TRUE assigns score onto 1bp position at centre of motif.
FALSE assigns every basepair the sum of scores of all overlapping motifs.

atCentre


Creates rlelist of pwm hits.<p></p><p>Motif score as an RLElist
</p>

The soGGi package provides a toolset to create genomic
interval aggregate/summary plots of signal or motif occurence
from BAM and bigWig files as well as PWM, rlelist, GRanges and
GAlignments Bioconductor objects. soGGi allows for
normalisation, transformation and arithmetic operation on and
between summary plot objects as well as grouping and subsetting
of plots by GRanges objects and user supplied metadata. Plots
are created using the GGplot2 libary to allow user defined
manipulation of the returned plot object. Coupled together,
soGGi features a broad set of methods to visualise genomics
data in the context of groups of genomic intervals such as
genes, superenhancers and transcription factor binding events.

Tom Carroll

soGGi

Visualise ChIP-seq, MNase-seq and motif occurrence as aggregate
plots Summarised Over Grouped Genomic Intervals

pwmToCoverage function

Creates rlelist of pwm hits.

Motif score as an RLElist

pwmToCoverage: PWM hits and motif scores as an RLElist

Description

Usage

Arguments

Value

Examples