getConsensusPeaks: Given a GRangeslist object with peaks for each samples,...

In ewymathe/testALTREinstall: Workflow for Identifying Regulatory Elements from Chromatin Accessibility Assay Data

Description

Given a GRangeslist object with peaks for each samples, determine the consensus peaks (found in at least N replicates, where N is input by the user) for each sample type

Usage

getConsensusPeaks(samplepeaks, minreps)

Arguments

samplepeaks	A GRangesList object comprising one GRanges object (peaks) for each sample (output of loadBEDFiles() function)
minreps	minimum number of replicate samples that a peak should be contained in to be called as a consensus peak. This cutoff will be applied to both samples.

Value

a list comprising: 1) a GRangeslist with one GRange for each sample type which contains consensus peaks 2) a summary statistic table

Examples

## Not run: 
dir <- system.file('extdata', package='ALTRE', mustWork=TRUE)
csvfile <- file.path(dir, 'lung.csv')
sampleinfo <- loadCSVFile(csvfile)
samplePeaks <- loadBedFiles(sampleinfo)
consPeaks <- getConsensusPeaks(samplepeaks = samplePeaks, minreps=2)

## End(Not run)

ewymathe/testALTREinstall documentation built on May 16, 2019, 9:42 a.m.