importData: Reading data from a BED or WIG file to RleList

In jianhong/trackViewer: A R/Bioconductor package with web interface for drawing elegant interactive tracks or lollipop plot to facilitate integrated analysis of multi-omics data

Reading data from a BED or WIG file to RleList

Description

Read a track object from a BED, bedGraph, WIG or BigWig file to RleList

Usage

importData(files, format = NA, ranges = GRanges())

Arguments

files	The path to the files to read.
format	The format of import file. Could be BAM, BED, bedGraph, WIG or BigWig
ranges	An object of GRanges to indicate the range to be imported

Value

a list of RleList.

Examples

#import a BED file
bedfile <- system.file("tests", "test.bed", package="rtracklayer",
                       mustWork=TRUE)
dat <- importData(files=bedfile, format="BED",
                  ranges=GRanges("chr7", IRanges(127471197, 127474697)))

##import a WIG file
wigfile <- system.file("tests", "step.wig", package = "rtracklayer",
                       mustWork=TRUE)
dat <- importData(files=wigfile, format="WIG", 
                  ranges=GRanges("chr19", 
                                 IRanges(59104701, 59110920)))

##import a BigWig file
if(.Platform$OS.type!="windows"){
  ##this is because we are using rtracklayer::import
  bwfile <- system.file("tests", "test.bw", package = "rtracklayer",
                        mustWork=TRUE)
  dat <- importData(files=bwfile, format="BigWig", 
                    ranges=GRanges("chr19", IRanges(1500, 2700)))
}

jianhong/trackViewer documentation built on Nov. 10, 2024, 10:33 a.m.