findconsensusRegions: Plot coverage of points or regions.

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

Description

Plot coverage of points or regions.

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

Usage

findconsensusRegions(testRanges, bamFiles = NULL, method = "majority",
  summit = "mean", resizepeak = "asw", overlap = "any",
  fragmentLength = NULL, NonPrimaryPeaks = list(withinsample = "drop",
  betweensample = "mean"))

summitPipeline(reads, peakfile, fragmentLength, readlength)

Arguments

testRanges	Named character vector of region locations
bamFiles	Named character vector of bamFile locations
method	Method to select reproducible summits to merge.
summit	Only mean avaialble
resizepeak	Only asw available
overlap	Type of overlap to consider for finding consensus sites
fragmentLength	Predicted fragment length. Set to NULL to auto-calculate
NonPrimaryPeaks	A list of parameters to deal with non primary peaks in consensus regions.
peakfile	GRanges of genomic intervals to summit.
reads	Character vector of bamFile location or GAlignments object
readlength	Read length of alignments.

Value

Consensus A GRanges object of consensus regions with consensus summits.

Summits A GRanges object of summits and summit scores.

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