This function takes a
GRanges-class object of aligned short reads
and removes pockets of reads that are stacked on top of each other based on the
maximum number of reads allowed to pileup in 'max.pileup' parameter.
A maximum number of reads overlapping each other to be kept.
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## Get some files that you want to load exampleFolder <- system.file("extdata", "example_results", package="breakpointRdata") infile <- list.files(exampleFolder, full.names=TRUE) ## Read in the reads breakP.obj <- get(load(infile)) frags <- breakP.obj$fragments ## Remove read spikes frags <- removeReadPileupSpikes(gr=frags)
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