I'm trying to plot genomic locus of interest. I'd be particularly interested in protein-coding genes. I've thought about loading Ensembl track using
ensGenes2 <- UcscTrack(genome = "hg19", chromosome = "chr19",
track = "ensGene", from = start, to = end, trackType = "GeneRegionTrack",
rstarts = "exonStarts", rends = "exonEnds", gene = "name",
symbol = "name", transcript = "name", strand = "strand",
fill = "#960000", name = "Ensembl Genes", showId=T, geneSymbol=T)
Somehow my feeling is that what I'm getting are also non-coding transcripts. Do you know how I can change it (to focus only on the coding ones)?
Another issue would be the symbols in the graph. Is there anyway that gviz can plot symbols like in the HUGO format?
I'd be really grateful for you help!