Obtaining Go slim terms from biomaRt
1
0
Entering edit mode
rubi ▴ 110
@rubi-6462
Last seen 6.3 years ago

Hi,

I'm trying to follow this post: GOseq at a specific level ? for obtaining GO slim data:

 

library(biomaRt)

library(org.Hs.eg.db)

mart <- useMart(biomart="ensembl", dataset="hsapiens_gene_ensembl")

go.slim <- getBM(attributes="goslim_goa_accession",mart=mart)[,1]

 

The last command hangs for ever.

Any idea what's wrong how if there

s another way to obtain GO slim terms?

 

> sessionInfo()

R version 3.3.1 (2016-06-21)

Platform: x86_64-pc-linux-gnu (64-bit)

Running under: CentOS Linux 7 (Core)


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=en_US.UTF-8       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  stats4    stats     graphics  grDevices utils     datasets 

[8] methods   base     


other attached packages:

[1] org.Hs.eg.db_3.4.0   AnnotationDbi_1.36.0 IRanges_2.8.0       

[4] S4Vectors_0.12.0     Biobase_2.34.0       BiocGenerics_0.20.0 

[7] biomaRt_2.30.0      


loaded via a namespace (and not attached):

[1] DBI_0.5-1      RCurl_1.95-4.8 RSQLite_1.0.0  bitops_1.0-6   XML_3.98-1.4  

> 

 

 

 

 

biomaRt goslim go • 1.4k views
ADD COMMENT
1
Entering edit mode
Mike Smith ★ 6.6k
@mike-smith
Last seen 29 minutes ago
EMBL Heidelberg

Your code works for me in approximately one minute, although the time does change when I use a different mirror.  If you'd like to try it using an alternative host you can do something like this:

mart <- useMart(biomart = "ENSEMBL_MART_ENSEMBL",
                dataset="hsapiens_gene_ensembl",
                host = "asia.ensembl.org")

go.slim <- getBM(attributes = "goslim_goa_accession", mart = mart)[,1]

The available Ensembl mirrors are www.ensembl.org, asia.ensembl.org, uswest.ensembl.org and useast.ensembl.org.  You can substitute any of those into the host argument to see if it performs any better for you.

ADD COMMENT

Login before adding your answer.

Traffic: 854 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6