text: user1499: I need a command in R to retrieve all human genes associated with a Gene Ontology entry. I tried to look for it online but did not find it.
  
  user77: Here's an example for the mouse genome:
  library(org.Mm.eg.db)
  select(org.Mm.eg.db, c("GO:0048406"), c("GENENAME","SYMBOL"), c("GO"))
  
  You get output like:
                                                      GENENAME SYMBOL
  1                                     pregnancy zone protein    Pzp
  2 nerve growth factor receptor (TNFR superfamily, member 16)   Ngfr
  3 nerve growth factor receptor (TNFR superfamily, member 16)   Ngfr
  4                                             neurotrophin 3   Ntf3
  5             neurotrophic tyrosine kinase, receptor, type 1  Ntrk1
  6            furin (paired basic amino acid cleaving enzyme)  Furin
  7              proprotein convertase subtilisin/kexin type 6  Pcsk6
  8                                                 sortilin 1  Sort1
  9                                      alpha-2-macroglobulin    A2m
  
  Edit: Given your comment that you want instead a list of all genes with a GO term associated with them (for human):
  library(org.Hs.eg.db) # Install it from bioconductor yourself
  unlist(as.list(org.Hs.egSYMBOL)[mappedkeys(org.Hs.egGO)])
  
  The mappedkey() part gets the index into the bimap of all entries with a valid GO mapping. That's then used to subset the symbol bimap (after converting to a list).
  
  user206: I guess the following code will help,
  source("https://bioconductor.org/biocLite.R")
  biocLite("biomaRt")
  library("biomaRt")
  ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
  #listAttributes(ensembl)
  mapping <- getBM(attributes = c("ensembl_gene_id", "hgnc_symbol", "go_id"), mart = ensembl)
  head(mapping)
  
  
original_text: 1499: <p>I need a command in R to retrieve all human genes associated with a Gene Ontology entry. I tried to look for it online but did not find it.</p>
   77: <p>Here's an example for the mouse genome:</p>
  
  <pre class="lang-r prettyprint-override"><code>library(org.Mm.eg.db)
  select(org.Mm.eg.db, c("GO:0048406"), c("GENENAME","SYMBOL"), c("GO"))
  </code></pre>
  
  <p>You get output like:</p>
  
  <pre><code>                                                    GENENAME SYMBOL
  1                                     pregnancy zone protein    Pzp
  2 nerve growth factor receptor (TNFR superfamily, member 16)   Ngfr
  3 nerve growth factor receptor (TNFR superfamily, member 16)   Ngfr
  4                                             neurotrophin 3   Ntf3
  5             neurotrophic tyrosine kinase, receptor, type 1  Ntrk1
  6            furin (paired basic amino acid cleaving enzyme)  Furin
  7              proprotein convertase subtilisin/kexin type 6  Pcsk6
  8                                                 sortilin 1  Sort1
  9                                      alpha-2-macroglobulin    A2m
  </code></pre>
  
  <p><strong>Edit</strong>: Given your comment that you want instead a list of all genes with a GO term associated with them (for human):</p>
  
  <pre><code>library(org.Hs.eg.db) # Install it from bioconductor yourself
  unlist(as.list(org.Hs.egSYMBOL)[mappedkeys(org.Hs.egGO)])
  </code></pre>
  
  <p>The <code>mappedkey()</code> part gets the index into the bimap of all entries with a valid GO mapping. That's then used to subset the symbol bimap (after converting to a list).</p>
   206: <p>I guess the following code will help,</p>
  
  <pre><code>source("https://bioconductor.org/biocLite.R")
  biocLite("biomaRt")
  library("biomaRt")
  ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
  #listAttributes(ensembl)
  mapping &lt;- getBM(attributes = c("ensembl_gene_id", "hgnc_symbol", "go_id"), mart = ensembl)
  head(mapping)
  </code></pre>
  