findconsensusRegions

summitPipeline

Named character vector of region locations

testRanges

Named character vector of bamFile locations

bamFiles

Method to select reproducible summits to merge.

method

summit

resizepeak

Type of overlap to consider for finding consensus sites

overlap

Predicted fragment length. Set to NULL to auto-calculate

fragmentLength

A list of parameters to deal with non primary peaks in consensus regions.

NonPrimaryPeaks

Character vector of bamFile location or GAlignments object

reads

peakfile

readlength


Plot coverage of points or regions.<p></p><p>Returns summits and summmit scores after optional fragment length prediction and read extension
</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

findconsensusRegions function

Plot coverage of points or regions.

Returns summits and summmit scores after optional fragment length prediction and read extension

findconsensusRegions: Plot coverage of points or regions.

Description

Usage

Arguments

Value