findOverlapsOverSamples {DEScan2} | R Documentation |
given in input a GRangeList where each element is a sample computes the coverage extending a both direction window of prefixed length.
findOverlapsOverSamples(samplePeaksGRangelist, extendRegions = 200, minOverlap = 0L, maxGap = -1L, zThresh = 10, verbose = FALSE, scorecolname = "z-score")
samplePeaksGRangelist |
given a granges list of samples finds the overlapping regions between them. |
extendRegions |
the number of bases to extend each region at its start and end. |
minOverlap |
the minimum overlap each peak needs to have. (see ChipPeakAnno::findOverlapsOfPeaks) |
maxGap |
the maximum gap admissible between the peaks. (see ChipPeakAnno::findOverlapsOfPeaks) |
zThresh |
a threshold value on z-score/scorecolname |
verbose |
verbose flag |
scorecolname |
character describing the name of the column within the peaks score. |
a GRanges of peaks overlapped and unique between samples.
(peaks.file <- system.file("extdata/peaks/RData/peaksGRL_all_files.rds", package="DEScan2")) peaksGRLFiles <- readRDS(peaks.file) (overlPeaks <- findOverlapsOverSamples(peaksGRLFiles))