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[1], end = lim[2],
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[1], to = lim[2],
transcriptAnnotation = "symbol", window = "auto",
cex.title = 1, fontsize = 10, type = "histogram")
Thanks for any help!!!
