[GenABEL-dev] function for conversion a plink format file to a GenABEL format file

[Nicola Pirastu]

Just to add my two cents,

there is also read.plink {snpMatrix} which returns a simple matrix, might require less from the RAM point of view.

Nicola

Dr. Nicola Pirastu PhD
Research Fellow
Medical Sciences, Chirurgical and Health Department
University of Trieste
Medical Genetics
IRCCS Burlo Garofolo
Via dell'Istria 65/1
34137 Italy
tel. +390403785539

Il giorno 22/nov/2013, alle ore 11:23, Maarten Kooyman <m.kooijman at erasmusmc.nl<mailto:m.kooijman at erasmusmc.nl>> ha scritto:


snpStats does have a GPL-3 licence, so we can use the code  and do whatever we want with it so long as we keep it under the same licence and give credit to to the owner/writer of the code.

Is it possible to adjust the snpStats code to dump the genotypes of the bed file directly into DatABEL format? This sound to me as the fastest(as in CPU time) option.

Maarten Kooyman

On 11/22/2013 11:08 AM, L.C. Karssen wrote:
> Thanks Maarten, that's a good finding. It does seem to return the data
> (incl. genotype data) in a list. I'm not sure how well that will work
> RAM-wise for large data sets. On the other hand the function does allow
> SNP selection, so maybe conversion could be done per chromosome.
>


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