readFilesAsGRangesList: readFilesAsGRangesList

In drighelli/DEScan2: Differential Enrichment Scan 2

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

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