[GenABEL-dev] eQTL functionality

[Yurii Aulchenko]

Hi Jimmie,

I completely agree with Lennart.

Some extra information:

1) I know some people working on eQTL find GenABEL::qtscore to be
helpful as it is quite fast compared to other alternatives

2) If you would be willing to work on developing specific eQTL
analysis functions, I will be glad to share my thoughts on that.
Basically, GenABEL::qtscore analysis of say 30,000 transcripts using
single processor would take about a week or two at the moment.
However, using some factorization tricks it should be possible to run
30,000 genome-wide analyses overnight.

best wishes,
Yurii

On Mon, Jun 27, 2011 at 6:15 PM, L.C. Karssen <l.karssen at erasmusmc.nl> wrote:
> Hi Jimmie,
>
> As far as I know, no one is working on eQTL analyses within the GenABEL
> project.
> Any contributions (and especially those in the form of code) are of
> course very welcome. Hopefully we can give you some hints on some of the
> more obscure parts of the code, if necessary.
>
>
> Best regards,
>
> Lennart Karssen.
>
> On vr, 2011-06-24 at 13:39 -0400, Chun (Jimmie) Ye wrote:
>> hi all,
>>
>> i was wondering if anyone is working on or has any interest in adding
>> some functionality for handling expression data and performing eQTL
>> analyses. in addition to the standard approaches, i have some
>> additional approaches in mind for adjusting for heterogeneity (both in
>> expression and population structure) that can be implemented. ideally,
>> it would leverage the data structures in genabel to handle the large
>> SNP arrays and possibly using some of the data structures in
>> bioconductor for handling expression data. i am willing to contribute
>> code.
>>
>> thanks,
>>
>> ~jimmie
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>
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