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# Custom track from the UCSC Table Browser content exported as Gene Transfer Format file
# Author : Sylvain Mareschal <maressyl@gmail.com>
# License : GPL3 http://www.gnu.org/licenses/gpl.html
track.table.GTF = function(
file,
name = NA,
attr = "split",
features = "exon",
quiet = FALSE,
.chromosomes,
...
)
{
# GTF parsing
gtf <- read.gtf(file=file, attr=attr, features=features, quiet=quiet)
# Filtering
if(!is.null(features)) gtf <- gtf[ gtf$feature %in% features ,]
# Consider "." strand as NA
gtf$strand <- factor(gtf$strand, levels=c("-","+"))
# Consider "seqname" as chromosome name
if(missing(.chromosomes)) { gtf$chrom <- factor(sub("^chr", "", gtf$seqname))
} else { gtf$chrom <- factor(sub("^chr", "", gtf$seqname), levels=.chromosomes)
}
gtf$seqname <- NULL
# Use "source" as name if unique
if(is.na(name) && length(unique(gtf$source)) == 1) {
name <- unique(gtf$source)
gtf$source <- NULL
}
# Track object
object <- track.table(gtf, .makeNames=TRUE, .name=name, ...)
return(object)
}
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