findPeaks: findPeaks

In drighelli/DEScan2: Differential Enrichment Scan 2

findPeaks

Description

This function calls peaks from bed or bam inputs using a variable window scan with a poisson model using the surrounding maxCompWinWidth (10kb) as background.

Usage

findPeaks(
  files,
  filetype = c("bam", "bed"),
  genomeName = NULL,
  binSize = 50,
  minWin = 50,
  maxWin = 1000,
  zthresh = 10,
  minCount = 0.1,
  minCompWinWidth = 5000,
  maxCompWinWidth = 10000,
  outputFolder = "Peaks",
  save = TRUE,
  force = TRUE,
  verbose = FALSE,
  sigwin = 10,
  onlyStdChrs = TRUE,
  chr = NULL,
  BPPARAM = BiocParallel::bpparam()
)

Arguments

files	Character vector containing paths of files to be analyzed.
filetype	Character, either "bam" or "bed" indicating format of input file.
genomeName	the code of the genome to use as reference for the input files. (cfr. constructBedRanges function parameters)
binSize	Integer size in bases of the minimum window for scanning, 50 is the default.
minWin	Integer indicating the minimum window size in bases notation.
maxWin	Integer indicating the maximum window size in bases notation.
zthresh	Cuttoff value for z-scores. Only windows with greater z-scores will be kept, default is 10.
minCount	A small constant (usually no larger than one) to be added to the counts prior to the log transformation to avoid problems with log(0).
minCompWinWidth	minimum bases width of a comparing window for Z-score.
maxCompWinWidth	maximum bases width of a comparing window for Z-score.
outputFolder	A string, Name of the folder to save the Peaks (optional) if the directory doesn't exist, it will be created. (Default is "Peaks")
save	Boolean, if TRUE files will be saved in a "./Peaks/chr*" directory created (if not already present) in the current working directory.
force	a boolean flag indicating if to force output overwriting.
verbose	if to show additional messages
sigwin	an integer value used to compute the length of the signal of a peak (default value is 10).
onlyStdChrs	a flag to work only with standard chromosomes. (cfr. constructBedRanges function parameters).
chr	if not NULL, a character like "chr#" indicating the chromosomes to use.
BPPARAM	object of class bpparamClass that specifies the back-end to be used for computations. See bpparam for details.

Value

A GRangesList where each element is a sample. Each GRanges represents the founded peaks and attached the z-score of the peak as mcols.

Examples

bam.files <- list.files(system.file("extdata/bam", package = "DEScan2"),
                        full.names = TRUE)

peaks <- findPeaks(files=bam.files[1], filetype="bam",
                        genomeName="mm9",
                        binSize=50, minWin=50, maxWin=1000,
                        zthresh=5, minCount=0.1, sigwin=10,
                        minCompWinWidth=5000, maxCompWinWidth=10000,
                        save=FALSE,
                        onlyStdChrs=TRUE,
                        chr=NULL,
                        verbose=FALSE)
head(peaks)

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