Constructor for GenomicAlignmentTrack — GenomicAlignmentTrack-class • igvR

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")

Value

A GenomicAlignmentTrack object

Details

Detailed description goes here

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)