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# Genes track from NCBI
# Author : Sylvain Mareschal <maressyl@gmail.com>
# License : GPL3 http://www.gnu.org/licenses/gpl.html
# Example file : ftp://ftp.ncbi.nih.gov/genomes/MapView/Homo_sapiens/sequence/current/initial_release/seq_gene.md.gz
track.genes.NCBI = function(
file,
name = "NCBI genes",
selection,
...
)
{
# Extraction
NCBI = utils::read.table(
file = file,
header = TRUE,
sep = "\t",
quote = "",
comment.char = "",
stringsAsFactors = FALSE
)
# Filtering out alternative assemblies
if(missing(selection)) stop("'selection' can not be missing. Choose between the following values : ", paste(unique(NCBI$group_label), collapse=", " ))
NCBI = NCBI[ NCBI$group_label %in% selection ,]
# Filtering out other features
NCBI = NCBI[ NCBI$feature_type == "GENE" ,]
# Filtering out special chromosomes
NCBI = NCBI[ !grepl(NCBI$chromosome, pattern="\\|") ,]
# Gene ID
geneId <- as.integer(sub("^.*GeneID:([0-9]+).*$", "\\1", NCBI$feature_id))
# Track object
object <- track.genes(
# Columns
name = NCBI$feature_name,
chrom = NCBI$chromosome,
start = as.integer(NCBI$chr_start),
end = as.integer(NCBI$chr_stop),
strand = factor(NCBI$chr_orient, levels=c("-","+")),
GeneID = geneId,
# Meta-data
.name = name,
...
)
return(object)
}
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