GWASTrack-class: Constructor for GWASTrack

In PriceLab/igvR: 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,
  color = "darkBlue",
  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
color	A css color name (e.g., "red" or "#FF0000"
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")
    }

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