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and   Annotation   available   between   bioc   bioconductor   Bioconductor   contents   convert   D2   db   dbconn   dbfile   dbschema   Dr   E2   eg   eg2acc   ensembl   Entrez   Example   from   gene   genes   H2   ids   Install   L2   let   library   list   Lite   ls   M2   mapped   mappedkeys   Now   O2   package   Packages   S2   see   source   T2   the   to   want   what   Zebrafish  

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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])

R/AnnotationPackages (last edited 2012-07-17 05:59:09 by ChrisSeidel)