[GenABEL-dev] faster polygenic

[Yurii Aulchenko]

Hi Xia,

Many thanks! The code looks good to me, and examples are very nice!

> - Reference list;
>

I suggest we change order to chronological, so your paper is 1st, then
Lee2001, Lee1996

> Perhaps the default 'conv' can be relaxed a bit. 1e-6 is good enough to me, and also 1e-8 might be two strict for some binary trait - getting a precision of 8 digits for binary data is too difficult, sometimes it might not even converge.
>

I agree. This will probably make it much faster. But we should tell
that in the documentation -- like "if you want really great
convergence, use 1e-8..."

> We are working on updating the 'hglm' package on CRAN, where I will make extracting internal variance-covariance matrix possible.
>

These are great news!

One thing which can make polygenic_hglm even more apparent news: I
understood that for the fixed effects, you get standard errors of the
estimates, correct? And these can be used for significance testing,
right? E.g. SNP or haplotype significance (if one puts a SNP as
covar). This would be extremely valuable, see discussion

http://forum.genabel.org/viewtopic.php?f=6&t=134

If easy, I suggest to pull fixed effects SE more close to the user,
and provide an example of doing test for a SNP. I really think this
will help polygenic_hglm to make to the news-lines -- and this is
something quite unique [not in 'polygenic', not, to my knowledge, for
FMM] :)

Yurii