[R] using pre-calculated coefficients and LP in coxph()?

[David Winsemius]

On Mar 13, 2011, at 1:32 PM, Dimitris Rizopoulos wrote:

> probably you want to use the 'init' argument and 'iter.max' control- 
> argument of coxph(). For example, for the Lung dataset, we fix the  
> coefficients of age and ph.karno at 0.05 and -0.05, respectively:
>
> library(survival)
>
> coxph(Surv(time, status) ~ age + ph.karno, data = lung,
>    init = c(0.05, -0.05), iter.max = 0)

>
>
> I hope it helps.
>
> Best,
> Dimitris
>
>
> On 3/13/2011 6:08 PM, Angel Russo wrote:
>> I need to force a coxph() function in R to use a pre-calculated set  
>> of beta
>> coefficients of a gene signature consisting of xx genes and the gene
>> expression is also provided of those xx genes.

I would have guessed (and that is all one can do without an example  
and better description of what the setting and goal might be) that the  
use of the offset capablity in coxph might be needed.

-- 
David.
>>
>> If I try to use "coxph()" function in R using just the gene  
>> expression data
>> alone, the beta coefficients and coxph$linear.predictors will  
>> change and I
>> need to use the pre-calcuated linear predictor not re-computed  
>> using coxph()
>> function. The reason is I need to compute a quantity that uses as  
>> it's input
>> the coxph() output but I need this output to be pre-calculated
>> beta-coefficients and linear.predictor.
>>
>> Any one can show me how to do this in R?
>>
>> Thanks a lot.

David Winsemius, MD
West Hartford, CT