GWASTrack-class: Constructor for GWASTrack

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

Constructor for GWASTrack

Description

GWASTrack creates an IGV manhattan track GWAS data

Usage

GWASTrack(
  trackName,
  table,
  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.
table	data.frame of 6 or more columns
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 GWASTrack object

Examples

  file <- system.file(package="igvR", "extdata", "gwas-5k.tsv")
  tbl.gwas <- read.table(file, sep="\t", header=TRUE, quote="")
  dim(tbl.gwas)
  track <- GWASTrack("gwas 5k", tbl.gwas, chrom.col=12, pos.col=13, pval.col=28)

  if(interactive()){
    igv <- igvR()
    setGenome(igv, "hg38")
    setBrowserWindowTitle(igv, "GWAS demo")
    displayTrack(igv, track)
    Sys.sleep(1)  # pause before zooming in
    showGenomicRegion(igv, "chr6:32,240,829-32,929,353")
    }

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