plotCombineAnnotatePeaks: Given the output from combineAnnotatePeaks, plot a barplot...

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

Description

Given the output from combineAnnotatePeaks, plot a barplot showing number of peaks before/after merging (only works if peaks were merged)

Usage

plotCombineAnnotatePeaks(conspeaks)

Arguments

conspeaks

output generated from combineAnnotatePeaks

Value

a ggplot

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)
plotConsensusPeaks(samplepeaks=consPeaks)
TSSannot <- getTSS()
consPeaksAnnotated <- combineAnnotatePeaks(conspeaks = consPeaks,
                                          TSS = TSSannot,
                                          merge = TRUE,
                                          regionspecific = TRUE,
                                          mergedistenh = 1500,
                                          mergedistprom = 1000)
plotCombineAnnotatePeaks(consPeaksAnnotated)

## End(Not run)

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