findPeaks: findPeaks
In DEScan2: Differential Enrichment Scan 2

Description Usage Arguments Value Examples

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.

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())

`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.

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

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)