[BioC] Genominator question

[Kasper Daniel Hansen]

I missed this question.

No, we have no plans to introduce use characters for chromosomes.
Originally, this was decided based on some ideas of
  1) reduced size in the database (not R)
  2) better speed in the database
  3) the ability to return matrices into R
1) is pretty hypothetical, but I believe 2) might very well be true.
And they are certainly true if we ever consider moving to a different
backend (away from SQLIte).  3) is actually somewhat important, for
efficiency purposes.

I think it would be too much work to get over the very minor
inconvenience of using integers for chromosomes (and as I see it - but
benchmarks to prove me wrong are always appreciated - we do get some
benefits from integers).  Especially in light of the fact that you
almost always have to do something with the chromosome names:
different sources might be using chr01, chr1, ch01, ch1 etc.

Kasper

On Thu, Apr 29, 2010 at 10:17 AM, rcaloger <raffaele.calogero at unito.it> wrote:
> I found Genominator very useful to store NGS data.
> However, I have a question concerning the data model.
> Data are saved in Genominator as:
> chr INTEGER, strand INTEGER, location INTEGER
> Although I can exchange X, Y and MT chromosome labels with INTEGERS, I
> wonder if  the chr definition can be changed from INTEGER to CHARACTER.
> Cheers
> Raffaele
>
> ----------------------------------------
> Prof. Raffaele A. Calogero
> Bioinformatics and Genomics Unit
> Dipartimento di Scienze Cliniche e Biologiche
> c/o Az. Ospedaliera S. Luigi
> Regione Gonzole 10, Orbassano
> 10043 Torino
> tel.   ++39 0116705417
> Lab.   ++39 0116705408
> Fax    ++39 0119038639
> Mobile ++39 3333827080
> email: raffaele.calogero at unito.it
>       raffaele[dot]calogero[at]gmail[dot]com
> www:   http://www.bioinformatica.unito.it
> Info: http://publicationslist.org/raffaele.calogero
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>