RemoteAlignmentTrack-class: Constructor for RemoteAlignmentTrack

RemoteAlignmentTrack-classR Documentation

Constructor for RemoteAlignmentTrack

Description

RemoteAlignmentTrack creates an IGV track for remote bam files

Usage

RemoteAlignmentTrack(
  trackName,
  bamUrl,
  bamIndex = NULL,
  trackHeight = 50,
  visibilityWindow = 30000,
  color = "gray"
)

Arguments

trackName

A character string, used as track label by igv, we recommend unique names per track.

bamUrl

The URL of a bam file

bamIndex

The URL of a bam index file. Defaults to <bamUrl>.bai

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 RemoteAlignmentTrack object


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