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I have a list of genes as row-names of my eset like:

iDs <- head(rownames(eset))

 [1] "LGI1"   "ATE1"   "NELL1"  "CCND1"  "FADD"   "PPFIA1" "ORAOV1" "FOXN4"  "NOVA1"  "PTGER2" "GPX2"   "DLK1"  
[13] "ZG16"   "MYH2"   "NPTX1"

How can I find GO info (more specific: function) of these genes in R?

This was my solution but I am not sure if I'm doing it right:

library (biomaRt)
mart = useMart("ensembl", dataset="hsapiens_gene_ensembl")
getGene( id = iDs[1] , type = "hgnc_symbol", mart = mart)

  hgnc_symbol hgnc_symbol                                                           description chromosome_name
1        LGI1        LGI1 leucine-rich, glioma inactivated 1 [Source:HGNC Symbol;Acc:HGNC:6572]              10
    band strand start_position end_position ensembl_gene_id
1 q23.33      1       93757809     93798174 ENSG00000108231

as I mentioned before what I want is to find out the function of these genes not the description or their location?

Any helps would be appreciated. Thanks,

thwd
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  • i have never used the `biomaRt` library when faced with a similar task. i have downloaded the GO database and parsed it. then looked up the genes i was interested in. – stas g Oct 12 '15 at 13:07
  • I am also have the same problem but I am not sure about my way! It's a bit confusing; have you found a solution for it? I've also asked the question here: http://stackoverflow.com/questions/35288238/gene-ontology-go-analysis-for-a-list-of-genes-with-entrezid-in-r – user3576287 Feb 09 '16 at 09:29

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