[GenABEL-dev] GenABEL: save.gwaa.data

[Yurii Aulchenko]

Dear Stephan, dear all,

My feeling is that this mail is more appropriate for the forum.genabel.org.

So, Stephan, may we please ask to direct your question there? In your
post, please explain, why you want the output of save.gwaa.data and
not something like what is provided by export.plink or export.merlin
and alike - basically, what you aim to.

Best wishes,
Yurii

On 5/27/11, Stephan Kolassa <Stephan.Kolassa at gmx.de> wrote:
> Dear GenABEL developers (Yurii?),
>
> I am trying to export quality-checked full genome data for analysis
> outside R (you may recall that I asked about modeling gene-environment
> interactions in GenABEL some months back). save.gwaa.data() seems to be
> exactly what I need. Unfortunately, I don't understand the human=FALSE
> encoding (I did my best, digging through the documentation and str()
> output), and human=TRUE exceeds my allocated memory, even after
> memory.limit(). You note on the save.gwaa.data help page that this could
> by addressed.
>
> My dataset after QC contains 413 IDs and 838230 SNPs. Do you think you
> could tweak save.gwaa.data() so it could output human=TRUE data on a
> standard Win XP laptop?
>
> If yes, how long would you think this would take you? (A couple of
> people are waiting for this, they would be very happy to have a rough
> idea about when we could move forward - and if they are too inpatient, I
> may need to find some other way to do this anyway.)
>
> Otherwise, do you have any documentation that would explain the
> snp.data-class in a little more detail, so I could try making sense out
> of human=FALSE data myself? Or is there any specific GenABEL source code
> I should be looking at?
>
> Sorry for imposing on you... and thank you once again for making GenABEL
> available!
>
> Best regards
> Stephan Kolassa
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