[BioC] retrieving external Gene IDs from TranscriptDB Object

[Stefanie Tauber]

Dear List,

I have created a TranscriptDB for yeast as follows:

library(GenomicFeatures)
library(biomaRt)

## create yeast DB
myDB <- makeTranscriptDbFromBiomart(biomart = "ensembl", dataset =
"scerevisiae_gene_ensembl", circ_seqs = c(DEFAULT_CIRC_SEQS, "Mito"))
myDBx <- cdsBy(myDB,by = "tx",use.names = TRUE)

Now, I would like to retrieve the external gene ids.
Is this the most generic way?

# select mart and dataset
mymart = useMart("ENSEMBL_MART_ENSEMBL", dataset =
"scerevisiae_gene_ensembl", host="www.ensembl.org")

# just a selection of transcripts

sel = names(myDBx)[5:6]

getBM(attributes=c("ensembl_transcript_id","external_gene_id"), values =
sel, filters = "ensembl_transcript_id", mart = mymart)


And, when creating a TranscriptDB From UCSC:


myDB1 <- makeTranscriptDbFromUCSC(genome = "hg19",tablename = "knownGene")
myDBx1 <- cdsBy(myDB1,by = "tx",use.names =TRUE)

What would be here the most generic way to retrieve the external gene IDs
for each transcript ID?

Best,
Stefanie


> sessionInfo()
R Under development (unstable) (2013-05-02 r62711)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=C                 LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
[1] biomaRt_2.16.0         GenomicFeatures_1.12.1 AnnotationDbi_1.22.3
[4] Biobase_2.20.0         GenomicRanges_1.12.2   IRanges_1.18.0
[7] BiocGenerics_0.6.0

loaded via a namespace (and not attached):
 [1] Biostrings_2.28.0  bitops_1.0-5       BSgenome_1.28.0    DBI_0.2-6
 [5] RCurl_1.95-4.1     Rsamtools_1.12.2   RSQLite_0.11.3    
rtracklayer_1.20.1
 [9] stats4_3.1.0       tools_3.1.0        XML_3.96-1.1       zlibbioc_1.6.0