Plot coverage of points or regions.

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Description

Plot coverage of points or regions.

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

Usage

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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.