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Constructor for GWASTrack

Source: R/GWASTrack.R
GWASTrack-class.Rd

GWASTrack creates an IGV manhattan track from GWAS data

Usage

GWASTrack(
  trackName,
  data,
  chrom.col,
  pos.col,
  pval.col,
  trackHeight = 50,
  autoscale = TRUE,
  minY = 0,
  maxY = 30
)

Arguments

trackName

A character string, used as track label by igv, we recommend unique names per track.

data

a data.frame or a url pointing to one, whose structure is described by chrom.col, pos.col, pval.col

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 column

trackHeight

numeric in pixels

autoscale

logical

minY

numeric for explicit (non-auto) scaling

maxY

numeric for explicit (non-auto) scaling

Value

A GWASTrack object

Examples

file <-
  # a local gwas file
  system.file(package = "igvShiny", "extdata", "gwas-5k.tsv.gz")
tbl.gwas <- read.table(file,
                       sep = "\t",
                       header = TRUE,
                       quote = "")
dim(tbl.gwas)
#> [1] 4949   34
track <-
  GWASTrack(
    "gwas 5k",
    tbl.gwas,
    chrom.col = 12,
    pos.col = 13,
    pval.col = 28
  )
getUrl(track)
#> [1] "/tmp/RtmplDjxGJ/tracks/file175329196024.gwas"

url <- "https://gladki.pl/igvShiny/gwas_sample.tsv.gz"
track <- GWASTrack(
  "remote url gwas",
  url,
  chrom.col = 3,
  pos.col = 4,
  pval.col = 10,
  autoscale = FALSE,
  minY = 0,
  maxY = 300,
  trackHeight = 100
)
getUrl(track)
#> [1] "https://gladki.pl/igvShiny/gwas_sample.tsv.gz"