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# Exon track from GENCODE
# Author : Sylvain Mareschal <maressyl@gmail.com>
# License : GPL3 http://www.gnu.org/licenses/gpl.html
# Example file : ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_29/gencode.v29.annotation.gtf.gz
track.exons.GENCODE = function(
file,
name = "GENCODE exons",
extra = c("gene_id", "gene_name", "exon_id"),
...
)
{
# Parse as a GTF file
track <- track.table.GTF(file, name=name, ...)
# Remove unwanted columns
mandatory <- c("name", "chrom", "strand", "start", "end", "transcript_id", "transcript_name")
columns <- union(mandatory, extra)
track$delColumns(setdiff(track$getColNames(), columns))
# Rename transcript column
track$setColNames("transcript_name", "transcript")
# Group by transcript
track$buildGroupPosition(groupBy="transcript")
track$buildGroupSize(groupBy="transcript")
# Use transript name to build name
track$fill(, "name", paste(sub("^ENST0+", "", track$extract(,"transcript_id")), track$extract(,"groupPosition"), sep="|"))
# Coerce to track.exons
object <- new("track.exons")
object$import(track)
return(object)
}
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