[R-sig-ME] Fitting known var-cov matrix in logistic regression model

David Duffy davidD at qimr.edu.au
Fri Apr 22 03:49:03 CEST 2011

On Thu, 21 Apr 2011, Margaret Mackinnon wrote:

> I want to estimate the relationship between population allele
> frequencies at a certain locus of interest and an environmental 
> variable.  The hypothesis is that this environmental variable has
> generated these different allele frequencies through differential
> selection pressure on a locus under balancing selection (i.e., there is
> negative selection which balances the differential positive selection on
> the allele of interest).   The allele frequencies are measured in 15
> different populations, as are the environmental variables.  However,
> this environmental variable has been aggregated at the population level
> so there are only 15 values that it can take.
>  The populations are genetically related to each other to different
> degrees and so I want to reflect this structuring by including in the
> model a variance-covariance matrix which captures this relatedness.  I
> estimated this variance-covariance matrix from a set of independent data
> on SNPs at a whole lot of putatively neutral loci that are not expected

The easiest way might be to use the SNP principal component scores for the
populations as covariates in an ordinary logistic regression. Otherwise
a GEE with your specified matrix, glmmPQL with a corSymm as per your model,

| David Duffy (MBBS PhD)                                         ,-_|\
| email: davidD at qimr.edu.au  ph: INT+61+7+3362-0217 fax: -0101  /     *
| Epidemiology Unit, Queensland Institute of Medical Research   \_,-._/
| 300 Herston Rd, Brisbane, Queensland 4029, Australia  GPG 4D0B994A v

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