GWASTrack-class: Constructor for GWASTrack

In paul-shannon/igvShiny: igvShiny: a wrapper of Integrative Genomics Viewer (IGV - an interactive tool for visualization and exploration integrated genomic data)

Constructor for GWASTrack

Description

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)
track <-
  GWASTrack(
    "gwas 5k",
    tbl.gwas,
    chrom.col = 12,
    pos.col = 13,
    pval.col = 28
  )
getUrl(track)

url <- "https://s3.amazonaws.com/igv.org.demo/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)

paul-shannon/igvShiny documentation built on Aug. 12, 2024, 7:41 p.m.