importScore: Reading data from a BED or WIG file

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

Description

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

Usage

importScore(
  file,
  file2,
  format = c("BED", "bedGraph", "WIG", "BigWig"),
  ranges = GRanges(),
  ignore.strand = TRUE
)

Arguments

file	The path to the file to read.
file2	The path to the second file to read.
format	The format of import file. Could be BED, bedGraph, WIG or BigWig
ranges	An object of GRanges to indicate the range to be imported
ignore.strand	ignore the strand or not when do filter. default TRUE

Value

a track object

See Also

See Also as importBam, track, viewTracks

Examples

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

##import a WIG file
wigfile <- system.file("tests", "step.wig", package = "rtracklayer",
                       mustWork=TRUE)
dat <- importScore(file=wigfile, format="WIG")

##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 <- importScore(file=bwfile, format="BigWig")
}

##import 2 file
wigfile1 <- system.file("extdata", "cpsf160.repA_+.wig", package="trackViewer",
                        mustWork=TRUE)
wigfile2 <- system.file("extdata", "cpsf160.repA_-.wig", package="trackViewer",
                        mustWork=TRUE)
dat <- importScore(wigfile1, wigfile2, format="WIG", 
                   ranges=GRanges("chr11", IRanges(122817703, 122889073)))

trackViewer documentation built on Feb. 11, 2021, 2 a.m.