loadBamTrackFromURL: load a bam track which, with index, is served up by http

In paul-shannon/igvShiny: igvShiny: a wrapper of Integrative Genomics Viewer (IGV - an interactive tool for visualization and exploration integrated genomic data)

load a bam track which, with index, is served up by http

Description

load a remote bam track

Usage

loadBamTrackFromURL(
  session,
  id,
  trackName,
  bamURL,
  indexURL,
  deleteTracksOfSameName = TRUE,
  displayMode = "EXPANDED",
  showAllBases = FALSE
)

Arguments

session	an environment or list, provided and managed by shiny
id	character string, the html element id of this widget instance
trackName	character string
bamURL	character string http url for the bam file, typically very large
indexURL	character string http url for the bam file index, typically small
deleteTracksOfSameName	logical, default TRUE
displayMode	character string, possible values are "EXPANDED"(default), "SQUISHED" or "COLLAPSED"
showAllBases	logical, show all bases in the alignment, default FALSE

Value

nothing

Examples

library(igvShiny)
demo_app_file <-
  system.file(package = "igvShiny", "demos", "igvShinyDemo.R")
if (interactive()) {
  shiny::runApp(demo_app_file)
}

paul-shannon/igvShiny documentation built on Aug. 31, 2024, 9:32 a.m.