GenomicAlignmentTrack-class {igvR} | R Documentation

## Constructor for GenomicAlignmentTrack

### Description

`GenomicAlignmentTrack` creates and `IGV` track for bed-like objects expressed as GRanges

### Usage

    GenomicAlignmentTrack(
      trackName,
      alignment,
      trackHeight = 50,
      visibilityWindow = 30000,
      color = "gray"
    )

### Arguments

`trackName` | A character string, used as track label by igv, we recommend unique names per track.
`alignment` | A GAlignments object
`trackHeight` | track height, typically in range 20 (for annotations) and up to 1000 (for large sample vcf files)
`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.
`color` | A character string, either a reconized color ("red") or a hex string ("#FF8532")

### Details

Detailed description goes here

### Value

A GenomicAlignmentTrack object

### Examples

      bamFile <- system.file(package="igvR", "extdata", "tumor.bam")
      which <- GRanges(seqnames = "21", ranges = IRanges(10400126, 10400326))
      param <- ScanBamParam(which=which, what = scanBamWhat())
      x <- readGAlignments(bamFile, use.names=TRUE, param=param)
      track <- GenomicAlignmentTrack("tumor", x)

[Package igvR version 1.12.0 Index]