GWASUrlTrack-class: Constructor for GWASUrlTrack

GWASUrlTrackR Documentation

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/igvR documentation built on Nov. 11, 2023, 8:26 p.m.