findOverlapsOverSamples {DEScan2} | R Documentation

## 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"
    )

### 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.

### 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))

[Package DEScan2 version 1.12.0 Index]