[GenABEL-dev] faster polygenic

[Yurii Aulchenko]

> I think the residuals from the mixed model is the most interesting stuff
> that will be passed into the next GWAS in GenABEL.
>
>
an object returned by polygenic contains

    h2an: A list supplied by the ‘nlm’ minimisation routine.  Of
          particular interest are elements "estimate" containing
          parameter maximal likelihood estimates (MLEs) (order: mean,
          betas for covariates, heritability, (polygenic + residual
          variance)). The value of twice negative maximum
          log-likelihood is returned as h2an\$minimum.

residualY: Residuals from analysis, based on covariate effects only;
          NOTE: these are NOT grammar "environmental residuals"!

   esth2: Estimate (or fixed value) of heritability

pgresidualY: Environmental residuals from analysis, based on covariate
          effects and predicted breeding value.

InvSigma: Inverse of the variance-covariance matrix, computed at the
          MLEs - these are used in ‘mmscore’ and ‘grammar’ functions.

    call: The details of call

InvSigma, residualY and pgresidualY are used in other analyses (e.g. mmscore
and grammar)

anyways, given estimates and kin-matrix are there, it is not great deal to
compute these values

Yurii
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