#http://www.ensembl.org/info/data/ftp/index.html
dataDirectory="./Data"
gtfFile=
# 'Mus_musculus.NCBIM37.67.gtf' #mm9
# 'Mus_musculus.GRCm38.83.gtf' #mm10
# 'Homo_sapiens.GRCh37.75.gtf' #hg19
'Homo_sapiens.GRCh38.83.gtf' #hg38
id=
# "mm9"
# "mm10"
# "hg19"
"hg38"
gtf = rtracklayer::import(file.path(dataDirectory, gtfFile))
seqlevelsStyle(gtf)='ucsc'
geneModels = data.frame(chromosome=as.character(chrom(gtf)),
start=as.numeric(start(gtf)),
end=as.numeric(end(gtf)),
width=width(gtf),
strand=strand(gtf),
feature=as.character(elementMetadata(gtf[,'source'])@listData$source),
gene=as.character(elementMetadata(gtf[,'gene_id'])@listData$gene_id),
exon=as.character(elementMetadata(gtf[,'transcript_id'])@listData$transcript_id),
transcript=as.character(elementMetadata(gtf[,'transcript_id'])@listData$transcript_id),
symbol=as.character(elementMetadata(gtf[,'gene_name'])@listData$gene_name))
geneModels = geneModels[geneModels$chromosome %in% paste0('chr',c(1:99,'X','Y')),]
save(geneModels, file=paste0("data/gm_", id, ".RData"))
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