findOverlapsOverSamples: findOverlapsOverSamples

In drighelli/DEScan2: Differential Enrichment Scan 2

findOverlapsOverSamples

Description

given in input a GRangeList where each element is a sample computes the coverage extending a both direction window of prefixed length.

Usage

findOverlapsOverSamples(
  samplePeaksGRangelist,
  extendRegions = 200,
  minOverlap = 0L,
  maxGap = -1L,
  zThresh = 10,
  verbose = FALSE,
  scorecolname = "z-score",
  coverageFlag = FALSE
)

Arguments

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.
coverageFlag	boolean indicating if to compute the scores in a coverage mode (sum of the reads of merged peak) or in a score mode (a normalized score across the merged peaks)

Value

a GRanges of peaks overlapped and unique between samples.

Examples

(peaks.file <- system.file("extdata/peaks/RData/peaksGRL_all_files.rds",
                            package="DEScan2"))
peaksGRLFiles <- readRDS(peaks.file)
(overlPeaks <- findOverlapsOverSamples(peaksGRLFiles))

drighelli/DEScan2 documentation built on March 21, 2023, 3:06 p.m.