plotgetcounts: Given the output from getCounts, plot a density plot of log2...

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

Description

Given the output from getCounts, plot a density plot of log2 RPKM values of regulation regions

Usage

plotgetcounts(countsconspeaks)

Arguments

countsconspeaks

output generated from getCounts

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 )

counts_consPeaks <- getCounts(annotpeaks = consPeaksAnnotated,
                             sampleinfo = sampleinfo,
                             reference = 'SAEC',
                             chrom = 'chr21')
plotgetcounts(counts_consPeaks)

## End(Not run)

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