[R] cox model for haplotypes
tlumley at u.washington.edu
Fri Mar 24 18:00:37 CET 2006
On Fri, 24 Mar 2006, SUBIRANA CACHINERO, ISAAC wrote:
> Anybody knows a function that can fit haplotype data to a Cox model.
> I've been searching it in the web without succeed.
> I use "haplo.stats" package, but unfortunatelly it's not possible to
> analyse survival data, amb I right?.
A relatively straightforward approach is to use haplo.em from the
haplo.stats package to impute the haplotypes. It will give you all the
possible haplotype pairs (diplotypes) for each individual, with
probabilities. You can then use all these possible diplotypes with the
probabilities as weights in coxph() and use cluster() to get the right
The haplo.ccs package does this for logistic regression, so you can follow
how it works for more details.
This approach will underestimate the standard errors of rare haplotypes,
especially in small samples, and is not fully efficient. The ideal
solution is Danyu Lin's semiparametric maximum partial likelihood
estimator, but I don't know of any implementations (the URL describe in
the paper lists the software as 'under development').
Thomas Lumley Assoc. Professor, Biostatistics
tlumley at u.washington.edu University of Washington, Seattle
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