Description Usage Arguments Value Examples
Given the output from getCounts, plot a density plot of log2 RPKM values of regulation regions
1 | plotgetcounts(countsconspeaks)
|
countsconspeaks |
output generated from getCounts |
a ggplot
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 | ## 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)
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