= R Annotation Packages from Bioconductor =

=== Example from Zebrafish ===
Install package
{{{
source("http://bioconductor.org/biocLite.R")
biocLite("org.Dr.eg.db")

# load package
library(org.Dr.eg.db)
}}}
Now let's list the contents to see what's available
{{{
> ls("package:org.Dr.eg.db")
 [1] "org.Dr.eg"                "org.Dr.eg.db"            
 [3] "org.Dr.eg_dbconn"         "org.Dr.eg_dbfile"        
 [5] "org.Dr.eg_dbInfo"         "org.Dr.eg_dbschema"      
 [7] "org.Dr.egACCNUM"          "org.Dr.egACCNUM2EG"      
 [9] "org.Dr.egALIAS2EG"        "org.Dr.egCHR"            
[11] "org.Dr.egCHRLENGTHS"      "org.Dr.egCHRLOC"         
[13] "org.Dr.egCHRLOCEND"       "org.Dr.egENSEMBL"        
[15] "org.Dr.egENSEMBL2EG"      "org.Dr.egENSEMBLPROT"    
[17] "org.Dr.egENSEMBLPROT2EG"  "org.Dr.egENSEMBLTRANS"   
[19] "org.Dr.egENSEMBLTRANS2EG" "org.Dr.egENZYME"         
[21] "org.Dr.egENZYME2EG"       "org.Dr.egGENENAME"       
[23] "org.Dr.egGO"              "org.Dr.egGO2ALLEGS"      
[25] "org.Dr.egGO2EG"           "org.Dr.egMAPCOUNTS"      
[27] "org.Dr.egORGANISM"        "org.Dr.egPATH"           
[29] "org.Dr.egPATH2EG"         "org.Dr.egPFAM"           
[31] "org.Dr.egPMID"            "org.Dr.egPMID2EG"
}}}

I want to convert a between ensembl gene ids and Entrez gene ids

{{{
# Get the entrez gene identifiers that are mapped to an ACCNUM
mapped_genes <- mappedkeys(org.Dr.egACCNUM)
# Convert to a list
eg2acc <- as.list(org.Dr.egACCNUM[mapped_genes])
}}}