Description Usage Arguments Value Examples
Given a GRangeslist object with peaks for each samples, determine the consensus peaks (found in at least N replicates, where N is input by the user) for each sample type
1 | getConsensusPeaks(samplepeaks, minreps)
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samplepeaks |
A GRangesList object comprising one GRanges object (peaks) for each sample (output of loadBEDFiles() function) |
minreps |
minimum number of replicate samples that a peak should be contained in to be called as a consensus peak. This cutoff will be applied to both samples. |
a list comprising: 1) a GRangeslist with one GRange for each sample type which contains consensus peaks 2) a summary statistic table
1 2 3 4 5 6 7 8 | ## 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)
## End(Not run)
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