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rubi
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@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 >