finalRegions: finalRegions

In drighelli/DEScan2: Differential Enrichment Scan 2

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",
  coverageFlag = FALSE,
  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.
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)
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)

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