finalRegions {DEScan2} | R Documentation |
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.
finalRegions(peakSamplesGRangesList, zThreshold = 20, minCarriers = 2, saveFlag = TRUE, outputFolder = "overlappedPeaks", verbose = FALSE, scorecolname = "z-score", BPPARAM = BiocParallel::bpparam())
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 |
a GRanges of selected overlapping peaks with z-score, n-peaks, k-carriers as mcols object.
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)