GWASUrlTrack-class: Constructor for GWASUrlTrack

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

Constructor for GWASUrlTrack

Description

GWASUrlTrack creates an IGV manhattan track GWAS data

Usage

GWASUrlTrack(
  trackName,
  url,
  chrom.col,
  pos.col,
  pval.col,
  colorTable = list(),
  autoscale = TRUE,
  min = 0,
  max = 10,
  trackHeight = 50,
  visibilityWindow = 1e+05
)

Arguments

trackName	A character string, used as track label by igv, we recommend unique names per track.
url	character
chrom.col	numeric, the column number of the chromosome column
pos.col	numeric, the column number of the position column
pval.col	numeric, the column number of the GWAS pvalue colum
colorTable	a named list of CSS colors, by chromosome name - exact matches to the names in the GWAS table.
autoscale	logical, controls how min and max of the y-axis are determined
min	numeric when autoscale is FALSE, use this minimum y
max	numeric when autoscale is FALSE, use this maximum y
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.

Value

A GWASUrlTrack object

Examples

  track <- GWASUrlTrack("GWAS from url",
                        "https://s3.amazonaws.com/igv.org.demo/gwas_sample.tsv.gz",
                         chrom.col=12, pos.col=13, pval.col=28)

    # note: this track is autoscaled.  apparently some infinite values in the file,
    # leading to a flat, low track.  reproduce this in static html, report issue to igv.js
    # temporary workaround: use the interactive track gear to set display range.

if(interactive()){
    igv <- igvR()
    setGenome(igv, "hg38")
    setBrowserWindowTitle(igv, "GWAS URL demo")
    displayTrack(igv, track)
    }

paul-shannon/IGV documentation built on Nov. 5, 2023, 2:09 p.m.