Question: Retrieving Dn Or Ds From Ensembl Using Biomart
1
gravatar for Max
5.1 years ago by
Max130
Max130 wrote:

I attempted to retrieve values of dn and ds for human/mouse gene comparisons in Ensembl using BiomaRt (R application), and get the following error (with mart defined as ensembl human reference genome):

t = getBM(attributes = "mmusculus_homolog_dn", filters = "hgnc_symbol", values = "GABRA6", mart = mart)
Error in `[.data.frame`(result, , attributes) : 
 undefined columns selected

In contrast, if I try to retrieve some other attribute, such as mouse gene id, it works (e.g.)

> t = getBM(attributes = "mmusculus_homolog_ensembl_gene", filters = "hgnc_symbol", values = "GABRA6", mart = mart)
> t
   [1] "ENSMUSG00000020428"

So it doesn't seem to be a syntax error. What am I doing wrong in calling the "mmmusculus...dn" attribute (and the same issue with ds)?

ensembl biomart • 2.1k views
ADD COMMENTlink modified 4.0 years ago by Biostar ♦♦ 20 • written 5.1 years ago by Max130
2
gravatar for Neilfws
5.1 years ago by
Neilfws48k
Sydney, Australia
Neilfws48k wrote:

Not sure why you are seeing that error. It works for me. Perhaps just some transient issue?

library(biomaRt)
mart.hs <- useMart("ensembl", "hsapiens_gene_ensembl")
getBM(attributes = "mmusculus_homolog_dn", filters = "hgnc_symbol", values = "GABRA6", mart = mart.hs)
#   mmusculus_homolog_dn
# 1               0.0459
getBM(attributes = "mmusculus_homolog_ds", filters = "hgnc_symbol", values = "GABRA6", mart = mart.hs)
#   mmusculus_homolog_ds
# 1               0.5686

My sessionInfo():

R version 3.0.3 (2014-03-06)
Platform: x86_64-pc-linux-gnu (64-bit)

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

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

other attached packages:
[1] biomaRt_2.18.0       BiocInstaller_1.12.0

loaded via a namespace (and not attached):
[1] RCurl_1.95-4.1 tools_3.0.3    XML_3.98-1.1
ADD COMMENTlink written 5.1 years ago by Neilfws48k

That's very strange. Perhaps the ensembl databases aren't being loaded correctly in the mart calls?

ADD REPLYlink written 5.1 years ago by Max130
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2444 users visited in the last hour