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# CNV track from the new version of DGV
# Author : Sylvain Mareschal <maressyl@gmail.com>
# License : GPL3 http://www.gnu.org/licenses/gpl.html
# Example file : http://dgvbeta.tcag.ca/dgv/app/downloads (Release Version)
track.CNV.DGV = function(
file,
name = "DGV CNV",
...
)
{
# Extraction
DGV <- utils::read.table(
file = file,
header = TRUE,
sep = "\t",
quote = "",
comment.char = "",
stringsAsFactors = FALSE
)
# Filtering out other features
DGV <- DGV[ DGV$varianttype == "CNV" ,]
# Track object
object <- track.CNV(
# Columns
name = as.character(DGV$variantaccession),
chrom = as.character(DGV$chr),
start = as.integer(DGV$start),
end = as.integer(DGV$end),
strand = factor(rep("+", nrow(DGV)), levels=c("-","+")),
type = factor(DGV$variantsubtype),
# Meta-data
.name = name,
...
)
return(object)
}
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