[BioC] Converting an Annbuilder object to a dataframe

[Daniel Brewer]

Thanks for the reply.  The reason I wanted to do this was so that I can
use some of the CGH packages with a limma object.  For this I need the
location information for all of the microarray probes and I thought that
the best way was to use the annotation package.  Is this misguided?  Are
there any alternatives

Many thanks again

Robert Gentleman wrote:
> Hi Daniel,
>   The main reason that they are not data.frames is that they don't fit
> into that kind of a box, so you are trying to do something that will
> require that you make specific choices along the way.
> 
>  Then, are you sure that is what you want to do? For example,
> 
>  library(hgu95av2)
>> v1=as.list(hgu95av2CHRLOC)
>> v1[1]
> $`986_at`
>        15
> -49288963
> 
> 
>  says this probe maps to chromosome 15, antisense strand position
> 49288963. You can find out the name (if that is what you want)
>  by
>  > hgu95av2SYMBOL$"986_at"
> [1] "CYP19A1"
> 
>  So all most all things you want can be achieved with fairly simple
> programs.
> 
>  If you really want to make data frames, then I suggest looking at
> functions like as.list and eapply, but there is not simple way to get
> what you want.
> 
>  An alternative is to make use of some of the interfaces to relational
> databases (eg RSQLite) as a way to get slightly more power than can be
> achieved easily from within R.  Annotation packages based on SQLite will
> be made available in the next release of Bioconductor and we are likely
> to shift over exclusively to them in the future (provided the
> performance is satisfactory).
> 
>  best wishes
>    Robert
> 
> 
> Daniel Brewer wrote:
>> Hello,
>>
>> I am attempting to use the "hgug4100a" library (built using AnnBuilder)
>> to integrate location information into a limma object.  The problem I am
>> having is how to change the annotation objects into a dataframe (once
>> there I can use the merge function).  Ideally I would have a dataframe
>> with the following columns:
>> Identifier    Chromosome    Location
>>
>> Anyone has any idea how to do this?  It is easy enough to change it into
>> the list but I need to strip out:
>> 1) The antisense location
>> 2) Reduce it to one entry per identifier
>> and the identifier has quotes round it
>>
>> Very confused about how to do this and any help would be appreciated.
>>
>> Thanks
>>
> 

-- 
**************************************************************

Daniel Brewer, Ph.D.
Email: daniel.brewer at icr.ac.uk