readFilesAsGRangesList {DEScan2} | R Documentation

## readFilesAsGRangesList

### Description

Takes in input the path of bam/bed files to process and stores them in a GRangesList object, named with filePath/filenames. (for lazy people)

### Usage

    readFilesAsGRangesList(
      filePath,
      fileType = c("bam", "bed", "bed.zip", "narrow", "broad"),
      genomeName = NULL,
      onlyStdChrs = TRUE,
      arePeaks = TRUE,
      verbose = TRUE
    )

### Arguments

`filePath` | the path of input files.
`fileType` | the type of the files (bam/bed/bed.zip/narrow/broad).
`genomeName` | the genome code to associate to the files. (recommended) (i.e. "mm9", "hg17")
`onlyStdChrs` | a flag to keep only standard chromosomes.
`arePeaks` | a flag indicating if the files contain peaks.
`verbose` | verbose output flag.

### Value

a GRangesList object

### Examples

    files.path <- system.file("extdata/bam", package="DEScan2")
    grl <- readFilesAsGRangesList(filePath=files.path, fileType="bam",
                                    genomeName="mm9", onlyStdChrs=TRUE,
                                    verbose=TRUE)
    class(grl)
    names(grl)
    grl

[Package DEScan2 version 1.12.0 Index]