plotDistCountAnalysis: Creates a boxplot to see the distribution of read counts in...

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

Description

Takes the rlog transformation of the RRKM (Reads Per Kilobase of transcript per Million) of the read counts of type-specific and shared regulatory regions and plots the distribution of those read counts in all sample types analyzed in the workflow.

Usage

plotDistCountAnalysis(analysisresults, counts)

Arguments

analysisresults	output generated from countanalysis() then categAltrePeaks()
counts	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')
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)
plotDistCountAnalysis(categaltre_peaks, counts_consPeaks)

## End(Not run)

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