I am not a card-carrying Bioinformatician or Biostatistician. At the risk of
demonstrating naivete let me ask "if you have reservations about snpper and
its durability why not query dbSNP?" :
http://www.ncbi.nlm.nih.gov/projects/SNP/


That may be easy for me to "say" since I don't have the skills to do the
programming, I am a pediatric otolaryngologist.


On 2/4/07, Vincent Carey 525-2265 <stvjc@channing.harvard.edu> wrote:
>
>
> > If I run an analysis which generates statistical tests on many SNPs I
> would
> > naturally want to get more details on the most significant SNPs.
> Directly
> > from within R one can get the information by loading RSNPer (from
> > Bioconductor) and simply issuing a command SNPinfo(2073285).
> Unfortunately,
> > the command cannot handle a vector and therefore only wants to do one at
> a
> > time.
> > I tried the lapply and sapply functions but was stymied temporarily
> > lapply(best.snp,SNPinfo) #where best.snp is a vector of SNPs
> > Error in FREQ[[1]] : subscript out of bounds [I do not know what that
> means]
> > Nevertheless, I found that one of the SNPs was causing this and could
> bypass
> > it by using the try function.
> >
> > lapply(best.snp,function(x) try(SNPinfo(x))) which let R continue
> > One can then extract numbers or values out of the resultant output but
> this
> > method lacks finesse and is not easy.
>
> looks pretty easy to me.  there is the nuisance of digging through
> the output but i have no use cases or -- to my knowledge, until you
> wrote -- any active users other than myself.  so little motivation
> to push further.
>
> additionally, snpper is not particularly well maintained (builds seem
> pretty old) and i think it is going to be replaced.  so i don't plan
> to put much more effort into it until i learn more about snpper.chip.org
> durability.
>
> >
> > Do you know of another method that would read the data and then write
> the
> > resultant data to a dataframe?
>
> i think you'll be able to do this with your lapply -- and contribute
> the code?
>
> >
> > Another very useful feature for which I would like to use the same
> treatment
> > is to use the SNPinfo as a way to get the gene information
> > lapply(best.snp,function(x) try(geneDetails(SNPinfo(x))))
>
> as above
>



-- 
Farrel Buchinsky
Mobile: (412) 779-1073

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