GenomicAlignmentTrack-class: Constructor for GenomicAlignmentTrack

GenomicAlignmentTrack-classR 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)


PriceLab/igvR documentation built on Sept. 6, 2022, 5:45 a.m.