Obtaining Go slim terms from biomaRt
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0
Entering edit mode
rubi ▴ 100
@rubi-6462
Last seen 4.0 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 • 890 views
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1
Entering edit mode
Mike Smith ★ 5.7k
@mike-smith
Last seen 2 hours ago
EMBL Heidelberg / de.NBI

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.

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