[BioC] from rat codelink to human locuslink

[Sean Davis]

Weiwei Shi wrote:
> Hi,
>
> I have 3 examples like this:
> Probe_ID        UniGene_ID      UniGene_Name
> AA799301_PROBE1 Rn.107913       Lgtn protein (DBSS)
> AA799313_PROBE1 Rn.32316        "sialyltransferase 10
> (alpha-2,3-sialyltransferase VI)"
> AA799329_PROBE1 Rn.112856       RIKEN cDNA 4632417K18 (Mm.) (DBSS)
>
> I think the UniGene_ID might work for the purpose of using biomartRt
> package (is it what you meant by biomart?). But the thing is, I look
> through the package intro but I did not find how to convert between
> species. Should I choose dataset for rat first, and then use rat2human
> conversion (i have a local program to do that but I am curious how
> biomartRt or other packages in R do this?)
Hi, Weiwei.  You'll probably want to look at the help pages for biomaRt 
(note the correct capitalization--sorry for the confusion).  To see a 
list of help pages, you can use the simple command:

 > help(package=biomaRt)

There are a couple of functions that look promising: getXref and 
getHomolog.  You might want to look into those a bit.

As for your probe ID's, it looks like they are a concatenation of a 
Genbank accession number and "PROBE1", so those could be useful.  
Unigene ID could also potentially be useful, but that depends a bit on 
how old the annotation is, as Unigene IDs change and are deleted on a 
regular basis as part of each new unigene build. 

Sean