I'm trying to visualize a region on the mouse chromosome (genome mm10) that contains a the Il7r gene. For the life of me I cannot figure out how to switch the gene name from the Ensembl format (Eg. ENMUSG000...) to the "common" gene name (Eg. Il7r). I've tried a number of things including changing the $symbol in object fm (code shown below) to trying different filters in the bm object (code shown below).
In the Gviz User guide is states:
"The internal .getBMFeatureMAP is helpful to set up the feature mapping which is necessary because Ensembl used to call the gene symbol field external_gene_id in that release."
I can get the gene symbol to display Il7r if I use the mm9 genome, but not with the mm10 genome, since parameters have been changed.
I've been using this (http://useast.ensembl.org/biomart/martview/ca12e7079979ccf12cb1f6269e0e623a) to try and figure the right symbol name to use.
I've been using this (http://useast.ensembl.org/biomart/martservice?redirect=no&type=filters&dataset=mmusculus_gene_ensembl&requestid=biomaRt&mart=ENSEMBL_MART_ENSEMBL&virtualSchema=default) to try and determine the right filter.
Here's the code I'm using:
ensembl <- useMart(biomart = "ENSEMBL_MART_ENSEMBL", dataset = "mmusculus_gene_ensembl", host = "useast.ensembl.org", archive = FALSE, ensemblRedirect = FALSE, verbose = TRUE) fm = Gviz:::.getBMFeatureMap() fm["symbol"] = "ensembl_gene_id" lim <- c(9450000, 9590000) bm <- BiomartGeneRegionTrack(genome = "mm10", chromosome='chr15', start=lim, end = lim, biomart = ensembl, filter=list("with_refseq_mrna"=TRUE), size = 4, name = "RefSeq", protein_coding = "black", col.line = NULL, cex = 7, collapseTranscripts = "longest", featureMap = fm) AT <- GenomeAxisTrack() plotTracks(list(bm, AT), from = lim, to = lim, transcriptAnnotation = "symbol", window = "auto", cex.title = 1, fontsize = 10, type = "histogram")
Thanks for any help!!!