findPeaks {DEScan2} | R Documentation

## 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)

[Package DEScan2 version 1.12.0 Index]