[GenABEL-dev] ld-based pruning

[Yurii Aulchenko]

Paul, I think this indeed may be interesting for other people as well; at
least I ran across similar problem a couple of times.

Could you please let us know more details about the implementation and your
thoughts about 'architecture' (is it / should it become a part of GenA,
ProbA, or something else, e.g. we have something called "GanABEL-suite
general" - smaller things not tied specifically to any package).

I also refer you to our set of devel-tutorials (
http://genabel.r-forge.r-project.org/) and some documents about our
policies (at http://www.genabel.org/developers) for general information

best wishes,
YA

On Fri, Mar 15, 2013 at 3:03 PM, P.S. de Vries <p.s.devries at erasmusmc.nl>wrote:

>  Dear all,****
>
> ** **
>
> In my research I constantly work with genetic risk scores based on a large
> amount of SNPs. Sometimes it is appropriate to prune the SNPs by LD before
> constructing the genetic risk score to obtain a set of independent SNPs.
> The most widely used function for this (plink --indep-pairwise) uses a
> sliding window to find pairs of SNPs in high LD with each other according
> to their R^2 and then removes one. However, it removes the SNP with the
> lowest minor allele frequency. In practice we may instead want to keep the
> SNP with the lowest p-value: i.e. the most important to us. This should
> lead to higher quality genetic risk scores.****
>
> ** **
>
> I have written a function that reads in a list of SNPs and then prunes it
> for LD by choosing which SNP to remove from a pair in high LD according to
> its position in the snp list. So the SNP that comes first in the SNP list
> will never be pruned out, and the second one only if it is in LD with the
> first one. The LD structure is based on your own data: it relies on the
> probabel configuration file for filepaths, and on databel for accessing the
> dosages.****
>
> ** **
>
> I initially did this just to apply it to my own data, but Lennart
> suggested it might be a nice addition to genabel. I am interested in
> developing this further if there is indeed interest in such a function. If
> so I will share the code and we can go from there.****
>
> ** **
>
> Let me know what you think,****
>
> ** **
>
> Paul****
>
> **
>
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