VariantTrack-class {igvR} | R Documentation

## Constructor for VariantTrack

### Description

`VariantTrack` creates an `IGV` track for VCF (variant call format) objects, either local or at a remote url

### Usage

    VariantTrack(trackName, vcf, trackHeight = 50, anchorColor = "pink",
      homvarColor = "rgb(17,248,254)", hetvarColor = "rgb(34,12,253)",
      homrefColor = "rgb(200,200,200)", displayMode = "EXPANDED",
      visibilityWindow = 1e+05)

### Arguments

`trackName` | A character string, used as track label by igv, we recommend unique names per track.
`vcf` | A VCF object from the VariantAnnotation package, or a list(url=x, index=y) pointing to a vcf file
`trackHeight` | track height, typically in range 20 (for annotations) and up to 1000 (for large sample vcf files)
`anchorColor` | CSS color name (e.g., "red" or "#FF0000") for the "anchoring" graphical segment in the track
`homvarColor` | CSS color name for homozygous variant samples, rgb(17,248,254) by default (~turquoise)
`hetvarColor` | CSS color name for heterzygous variant samples, rgb(34,12,253) by default (~royalBlue)
`homrefColor` | CSS color names for homozygous reference samples, rgb(200,200,200) by default (~lightGray)
`displayMode` | "COLLAPSED", "EXPANDED", or "SQUISHED"
`visibilityWindow` | Maximum window size in base pairs for which indexed annotations or variants are displayed. Defaults: 1 MB for variants, whole chromosome for other track types.

### Details

Detailed description goes here

### Value

A VariantTrack object

### Examples

        #----------------------------
        #  first, from a local file
        #----------------------------

    f <- system.file("extdata", "chr22.vcf.gz", package="VariantAnnotation")
    roi <- GRanges(seqnames="22", ranges=IRanges(start=c(50301422, 50989541),
                                                  end=c(50312106, 51001328),
                                                  names=c("gene_79087", "gene_644186")))
    vcf.sub <- VariantAnnotation::readVcf(f, "hg19", param=roi)
    track.local <- VariantTrack("chr22-tiny", vcf.sub)

        #----------------------------
        # now try a url track
        #----------------------------

    data.url <- sprintf("%s/%s", "https://s3.amazonaws.com/1000genomes/release/20130502",
                                   "ALL.wgs.phase3_shapeit2_mvncall_integrated_v5b.20130502.sites.vcf.gz")
    index.url <- sprintf("%s.tbi", data.url)
    url <- list(data=data.url, index=index.url)

    track.url <- VariantTrack("1kg", url)

[Package igvR version 1.6.1 Index]