You could do a weighted cox ph model, with possible haplotype configurations for each subject weighted by their posterior probabilities given genotype data.
Are your markers SNPs? If so you can use a utility function from the hapassoc package to get started. For example, if your data is in a dataframe dat, with nsnp SNPs in the last nsnps columns, you could create an augmented data frame (augmented by pseudo-individuals for each subject with ambiguous phase) with library(hapassoc) ph<-pre.hapassoc(dat,nsnps) augdat<-cbind(ph$nonHaploDM,ph$haploDM) wts<-ph$wt and then use coxph with augdat as the data frme and wts as the weights. See ?pre.hapassoc for details on accepted formats for the SNP data. Brad -- Brad McNeney Statistics and Actuarial Science Simon Fraser University On Tue, Oct 26, 2010 at 12:01 PM, David Winsemius <dwinsem...@comcast.net> wrote: > > On Oct 26, 2010, at 8:57 AM, sr500 wrote: > >> >> Hello, >> >> I was wondering if anyone knew of a function that fits haplotype data into >> a >> cox proportional hazard model. I have computed my Haplotype frequencies >> using the haplo.stats package. I have also been using the haplo.glm >> function >> but this is a linear regression and is not quite what I am looking for… >> > > I think you need to describe your data situation more completely and ideally > would include a small extract of your data to allow testing and > illustration. Cox proportional hazards models are typically used to analyze > time to event data and you have not alluded to any "events". > > -- > David. > >> Thank you very much, >> SR >> >> -- >> View this message in context: >> http://r.789695.n4.nabble.com/Cox-Proportional-Models-and-Haplotypes-tp3013989p3013989.html >> Sent from the R help mailing list archive at Nabble.com. > > ______________________________________________ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
