[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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