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cox model for haplotypes
2 messages · SUBIRANA CACHINERO, ISAAC, Thomas Lumley
On Fri, 24 Mar 2006, SUBIRANA CACHINERO, ISAAC wrote:
Hi, 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 standard errors. 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 Thomas Lumley Assoc. Professor, Biostatistics tlumley at u.washington.edu University of Washington, Seattle