[Bioc-devel] mapping vector of gene ids to gene symbols

[Marc Carlson]

Hi Michael,

The fact that duplicate keys are not being allowed in OrganismDb objects 
is an inconsistency that I will be looking into.  That is, if you do the 
same thing with orgDb or TranscriptDb objects, duplicates are allowed 
and passed along.  So I plan to fix this. I have checked in a 
preliminary fix to the devel branch.

The NAs on the other hand though have always been dropped from select 
methods since it doesn't usually make sense to include them in the 
output.  I can explore the possibility of doing something with an extra 
argument to support a much more strict interpretation of the keys, but 
it would have to error out if there are one to many mappings.


  Marc


On 06/18/2014 06:03 AM, Michael Lawrence wrote:
> Let's say I have a vector of gene IDs where some are NA, and are some are
> repeated, and I want to map them to gene symbols, where I get NAs for the
> NA IDs or IDs without a symbol. What is the best way to do this?
>
> I tried select() but it gave me a table with unique entries; not very
> convenient. It also does not handle NAs. And totally breaks with duplicates
> using the GENEID key type (kind of works with ENTREZID):
>
> select(Homo.sapiens, GENEID, "SYMBOL", "GENEID")
> Error in `[[<-`(`*tmp*`, name, value = list(GENEID = c("245938", "245939",
> :
>    269 elements in value to replace 1312 elements
>
> Also tried the venerable mget(GENEID, org.Hs.egSYMBOL, ifnotfound=NA), but
> this returns a list and fails with NAs.
>
> What would be nice is something like:
>
> map(Homo.sapiens, GENEID, "SYMBOL", "GENEID", OneToOneOrNone)
>
> where OneToOneOrNone is an assertion that I expect the mappings to be
> one-to-one, so it will unlist() or whatever and throw an error if the
> assertion fails. It should return NA for anything not found, and for any NA
> GENEID. Does something like this already exist?
>
> Michael
>
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