readFilesAsGRangesList: readFilesAsGRangesList
In DEScan2: Differential Enrichment Scan 2

Description Usage Arguments Value Examples

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)

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

`filePath`	the path of input files.
`fileType`	the type of the files (bam/bed/bed.zip).
`genomeName`	the genome code to associate to the files. (reccommended) (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.

a GRangesList object

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