Description Usage Arguments Examples
Creates a CSV file with genomic regions annoted as promotor or enhances categorized by cell type
1 | writeAnnotatedRegions(countsPeaks, con)
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countsPeaks |
output generated from getCounts() |
con |
connection filepath |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 | ## 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)
TSSannot <- getTSS()
consPeaksAnnotated <- combineAnnotatePeaks(conspeaks = consPeaks,
TSS = TSSannot,
merge = TRUE,
regionspecific = TRUE,
mergedistenh = 1500,
mergedistprom = 1000 )
#Need to run getcounts on all chromosomes
countsPeaks <- getcounts(annotpeaks = consPeaksAnnotated,
csvfile = csvfile,
reference = 'SAEC')
con <- "annotatedRegions.csv"
writeAnnotatedRegions(countsPeaks, con)
## End(Not run)
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