[GenABEL-dev] faster polygenic

[Yurii Aulchenko]

>> Absolutely, this was what I though about. Polygenic-FMM-Object should
>> comply to 'polygenic' format -- meaning it should have a few slots
>> named in particular way, but not necessarily all, and can contain
>> extra slots with info not in standard polygenic (e.g. I remember you
>> derive something big during null-herit estimation, which is not in
>> standard polygenic). Then we could thinking of coming up with
>> 'consolidated' polygenic-class at the end, or decide this is not worth
>> effort :)
>
> great - I will look at polygenic-class to see what I need to add
>

What may be a good plan -- if you make fixed effects estimates, and h2
+ total var (or anything which can help computing these) visible, we
already can use that for mmscore -- along the lines with
'polygenic_hglm'

https://r-forge.r-project.org/scm/viewvc.php/pkg/GenABEL/R/polygenic_hglm.R?view=markup&revision=663&root=genabel

where I recover all other staff from these parameters (see lines after
the call "res_hglm <- hglm(y = y, X = desmat, Z = L, family = family,
... )", where I fake much of the 'polygenic' object from these
params).

Surely, most of the things you already compute inside, and eventually
it all can be done better and much faster; but why not having
something working and run some comparison already.

bw,
Yurii