constructBedRanges: constructBedRanges

In drighelli/DEScan2: Differential Enrichment Scan 2

constructBedRanges

Description

Constructs a GRanges object from a bam/bed/bed.zip file in a consistent way.

Usage

constructBedRanges(
  filename,
  filetype = c("bam", "bed", "bed.zip", "narrow", "broad"),
  genomeName = NULL,
  onlyStdChrs = FALSE,
  arePeaks = FALSE,
  verbose = FALSE
)

Arguments

filename	the complete file path of a bam?bed file.
filetype	the file type bam/bed/bed.zip/narrow/broad.
genomeName	the name of the genome used to map the reads (i.e. "mm9"). N.B. if NOT NULL the GRanges Seqinfo will be forced to genomeName Seqinfo (needs Internet access, but strongly suggested!)
onlyStdChrs	flag to keep only standard chromosome.
arePeaks	flag indicating if the file contains peaks.
verbose	flag to obtain verbose output.

Value

a GRanges object.

Examples

files <- list.files(system.file("extdata/bam/", package="DEScan2"),
                    pattern="bam$", full.names=TRUE)
bgr <- constructBedRanges(files[1], filetype="bam", genomeName="mm9",
                            onlyStdChrs=TRUE)
bgr

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