[BioC] biomaRt inter_paralog attribute error

Remo Sanges noncoding at gmail.com
Thu May 23 22:32:28 CEST 2013


Dear BioConducters,

I am experiencing errors from the biomaRt package when I try to get 
inter_paralog_ensembl_gene. The strange error I get is the following:

Error in `[.data.frame`(result, , attributes) :
   undefined columns selected

It happens when I use the ensembl mart asking for all the attributes 
involving xxxxx_inter_paralog_ensembl_gene even if they are correctly 
listed when I ask for listAttributes(). The behaviour is the same if I 
use the very last version biomart at ensembl setting host="ensembl.org".

Am I doing something wrong?

Here is a sample code of which the last line reproduces the error:

library('biomaRt')
db = 'hsapiens_gene_ensembl'
mart = useMart('ensembl',dataset=db)
hom = 
getBM(attributes=c('ensembl_gene_id','mmusculus_homolog_ensembl_gene'),mart=mart)
ipa = 
getBM(attributes=c('ensembl_gene_id','mmusculus_inter_paralog_ensembl_gene'),mart=mart)

Here are my session info:

R version 3.0.0 (2013-04-03)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] biomaRt_2.16.0

loaded via a namespace (and not attached):
[1] RCurl_1.95-4.1 tools_3.0.0    XML_3.95-0.2

Many Thanks

Kind Regards

ERemo

-- 
Remo Sanges - Ph.D.
Bioinformatics - Animal Physiology and Evolution
Stazione Zoologica Anton Dohrn
Villa Comunale, 80121 Napoli - Italy
+39 081 5833428



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