GenomicAlignmentTrack-class: Constructor for GenomicAlignmentTrack
In igvR: igvR: integrative genomics viewer

Description Usage Arguments Details Value Examples

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

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

`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")

Detailed description goes here

A GenomicAlignmentTrack object

  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)