finalRegions {DEScan2}R Documentation

finalRegions

Description

Align peaks to form common regions then filter regions for presence in multiple replicates taking in input a GRangesList where each element is a sample of called peaks.

Usage

finalRegions(
  peakSamplesGRangesList,
  zThreshold = 20,
  minCarriers = 2,
  saveFlag = TRUE,
  outputFolder = "overlappedPeaks",
  verbose = FALSE,
  scorecolname = "z-score",
  BPPARAM = BiocParallel::bpparam()
)

Arguments

peakSamplesGRangesList

named GRangesList where each element is a sample of called peaks. A score mcols values is needed for each GRanges. The scorecolname param can be used as reference name for the score. (tipically returned by findPeaks function).

zThreshold

a minimum threshold for the z score. All peaks lesser than this value will be ignored.

minCarriers

a threshold of minimum samples (carriers) for overlapped regions.

saveFlag

a flag for saving results in a tsv file.

outputFolder

the directory name to store the bed file.

verbose

verbose output.

scorecolname

character describing the name of the column within the peaks score.

BPPARAM

object of class bpparamClass that specifies the back-end to be used for computations. See bpparam for details.

Value

a GRanges of selected overlapping peaks with z-score, n-peaks, k-carriers as mcols object.

Examples

peak.path <- system.file("extdata/peaks/RData/peaksGRL_all_files.rds",
                            package="DEScan2")
grl <- readRDS(peak.path)
grl

regionsGR <- finalRegions(peakSamplesGRangesList=grl, zThreshold=1,
                        minCarriers=3, saveFlag=FALSE, verbose=TRUE)

[Package DEScan2 version 1.13.0 Index]