[R] Manage huge database

[Martin Morgan]

"José E. Lozano" <lozalojo at jcyl.es> writes:

>> Maybe you've not lurked on R-help for long enough :) Apologies!
>
> Probably.
>
>> So, how much "design" is in this data? If none, and what you've
>> basically got is a 2000x500000 grid of numbers, then maybe a more raw
>
> Exactly, raw data, but a little more complex since all the 500000 variables
> are in text format, so the width is around 2,500,000.
>
>> http://cran.r-project.org/web/packages/RNetCDF/index.html
>> http://cran.r-project.org/web/packages/hdf5/index.html
>
> Thanks, I will check. Right now I am reading line by line the file. It's
> time consuming, but since I will do it only once, just to rearrange the data
> into smaller tables to query, it's ok.
>
>> Thinking back to your 4GB file with 1,000,000,000 entries, that's
>> only 3 bytes per entry (+1 for the comma). What is this data? There
>> may be more efficient ways to handle it.
>
> Is genetic DNA data (individuals genotyped), hence the large amount of
> columns to analyze.

The Bioconductor package snpMatrix is designed for this type of
data. See

http://www.bioconductor.org/packages/2.2/bioc/html/snpMatrix.html

and if that looks promising

> source('http://bioconductor.org/biocLite.R')
> biocLite('snpMatrix')

Likely you'll quickly want a 64 bit (linux or Mac) machine.

Martin

> Best Regards,
> Jose Lozano
> ------------------------------------------
> Jose E. Lozano Alonso
> Observatorio de Salud Pública.
> Direccion General de Salud Pública e I+D+I.
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>
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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