GenomicAlignmentTrack-class: Constructor for GenomicAlignmentTrack

In paul-shannon/IGV: igvR: integrative genomics viewer

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)

paul-shannon/IGV documentation built on Nov. 17, 2024, 11:55 p.m.