[BioC] topGO genes associated with GO terms

Wolfgang Huber whuber at embl.de
Mon Jun 9 17:14:53 CEST 2014


Agnieszka

it depends on the species and gene identifier system that you are looking for. 
Assuming that you want to get Ensembl Gene-IDs in Homo Sapiens, then something like the below will do.
  
library('org.Hs.eg.db')
key = 'GO:0043586'
columns = c('ENSEMBL', 'GENENAME')
s = select(org.Hs.eg.db, key, columns, keytype='GO')
print(s)

There are also alternative facilities in the biomaRt package.

	Wolfgang


Il giorno 07 Jun 2014, alle ore 00:55, Agnieszka Golicz [guest] <guest at bioconductor.org> ha scritto:

> Hello,
> 
> Is it possible to recover a full list of genes associated with a significantly enriched GO term?
> 
> I am using custom annotation in the GO2gene format.
> 
> 
> Best wishes,
> Agnieszka
> 
> -- output of sessionInfo(): 
> 
>> sessionInfo()
> R version 3.0.1 (2013-05-16)
> Platform: x86_64-unknown-linux-gnu (64-bit)
> 
> 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=C                 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  stats     graphics  grDevices utils     datasets  methods
> [8] base
> 
> other attached packages:
> [1] topGO_2.12.0         SparseM_1.03         GO.db_2.9.0
> [4] RSQLite_0.11.4       DBI_0.2-7            AnnotationDbi_1.22.6
> [7] Biobase_2.20.1       BiocGenerics_0.6.0   graph_1.38.3
> 
> loaded via a namespace (and not attached):
> [1] grid_3.0.1      IRanges_1.18.4  lattice_0.20-27 stats4_3.0.1
> [5] tools_3.0.1
> 
> 
> --
> Sent via the guest posting facility at bioconductor.org.
> 
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