Given a LocalPeaks object, merge peaks which are in the same sample and are
separated by no more than
gap base pairs. When two non-overlapping
peaks are merged, a new peak is created which starts at the starting position
of the first peak and ends at the ending position of the second peak,
spanning the range of both peaks and the gap between them.
Numeric value, specifying the threshold distance for merging. Peaks in the same sample which are within this many bp of each other will be merged.
The LocalPeaks object that was provided as input, with nearby peaks merged
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samples <- c("E068", "E071", "E074", "E101", "E102", "E110") bedfiles <- system.file("extdata", paste0(samples, ".H3K4me3.bed"), package = "chromswitch") metadata <- data.frame(Sample = samples, H3K4me3 = bedfiles, stringsAsFactors = FALSE) lpk <- retrievePeaks(H3K4me3, metadata = metadata, region = GRanges(seqnames = "chr19", ranges = IRanges(start = 54924104, end = 54929104))) reducePeaks(lpk, gap = 300)
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