R help - Oct 2010 - Cox Proportional Models and Haplotypes

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? 

Thank you very much,
SR

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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.

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
<dwinsemius at 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.
>
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