plotCountAnalysis: 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

plotCountAnalysis(altrepeakscateg)

Arguments

altrepeakscateg

output generated from countanalysis() then categAltrePeaks()

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')
altre_peaks <- countanalysis(counts = counts_consPeaks,
                             pval = 0.01,
                             lfcvalue = 1)
categaltre_peaks <- categAltrePeaks(altre_peaks,
                                    lfctypespecific = 1.5,
                                    lfcshared = 1.2,
                                    pvaltypespecific = 0.01,
                                    pvalshared = 0.05)
plotCountAnalysis(categaltre_peaks)

## End(Not run)

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