importScore {trackViewer} | R Documentation

## Reading data from a BED or WIG file

### 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

### Author(s)

Jianhong Ou

### 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)))

[Package trackViewer version 1.14.1 Index]