GWASTrack-class | R Documentation |
GWASTrack
creates an IGV
manhattan track from GWAS data
GWASTrack(
trackName,
data,
chrom.col,
pos.col,
pval.col,
trackHeight = 50,
autoscale = TRUE,
minY = 0,
maxY = 30
)
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 |
A GWASTrack object
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)
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