| readFilesAsGRangesList {DEScan2} | R Documentation |
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)
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