Constructor for GWASUrlTrack — GWASUrlTrack • igvR

GWASUrlTrack creates an IGV manhattan track GWAS data

Usage

GWASUrlTrack(
  trackName,
  url,
  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.
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
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 GWASUrlTrack object

Examples


    #----------------------------
    #  first, from a local file
    #----------------------------

  file <- system.file(package="igvR", "extdata", "tbl.mef2cGWAS.variants.RData")
  tbl.gwas <- get(load(file))
  dim(tbl.gwas)  #  32 6
#> [1] 178   9
  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)


    #------------------------------------------
    #  show the relevant portion of the genome
    #------------------------------------------

  shoulder <- 10000
  roi <- with(tbl.gwas, sprintf("%s:%d-%d", CHR[1], min(BP)-shoulder, max(BP) + shoulder))
  # showGenomicRegion(igv, roi)

  # displayTrack(igv, track)