A small set of functions aiding in the use of the annotation packages in Bioconductor. Developed for the organism annotation packages org.Bt.eg.db and org.Hs.eg.db, its main function is when doing one- and two-step translation between different gene/protein identifers such as entrez and Ensembl.

The package can be downloaded here, but when BioC 2.8 is released (April 14th), it is recommended to get an updated edition via BioC:

source("http://bioconductor.org/biocLite.R")
biocLite("AnnotationFuncs")

Go the the packages page on BioConductor: http://bioconductor.org/packages/release/bioc/html/AnnotationFuncs.html.

The main function is “translate”, here is an example:

library(AnnotationFuncs)
library(org.Bt.eg.db)
symbols <- c("SERPINA1","KERA","CD5")
refseq <- translate(symbols, from=org.Bt.egSYMBOL2EG, to=org.Bt.egREFSEQ)
refseq
$SERPINA1
[1] "NM_173882" "NP_776307"
 
$KERA
[1] "NM_173910" "NP_776335"
 
$CD5
[1] "NM_173899" "NP_776324"
 
pickRefSeq(refseq, priorities=c('NP','XP'), reduce='all')
$SERPINA1
[1] "NP_776307"
 
$KERA
[1] "NP_776335"

Note: “translate” is a common name and the function might be masked by another package. If problems do occur, try calling the function by the package, i.e. AnnotationFuncs::translate(…) For more information, from R execute ?AnnotationFuncs and ?translate

From initial release to 1.3.0, I have added a function, getHomolog, for use on the BioConductor Homology data packages from INPARANOID. The function getHomolog performs roughly 100 times quicker than the builtin methods.

• Curent versions:
  • Windows binaries: annotationfuncs_1.3.0.zip
  • Unix build: annotationfuncs_1.3.0.tar.gz

• Previous versions of the package:
  • Windows binaries: annotationfuncs_0.9.9.zip
  • Unix build: annotationfuncs_0.9.9.tar.gz
  • Windows binaries: annotationfuncs_0.1.zip
  • Unix build: annotationfuncs_0.1.tar.gz