findconsensusRegions {soGGi} | R Documentation

## Plot coverage of points or regions.

### 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.

[Package soGGi version 1.12.0 Index]