R help - Mar 2011 - using pre-calculated coefficients and LP in coxph()?

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.

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.

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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.
>
> 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.
>
> 	[[alternative HTML version deleted]]
>
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>
-- 
Dimitris Rizopoulos
Assistant Professor
Department of Biostatistics
Erasmus University Medical Center

Address: PO Box 2040, 3000 CA Rotterdam, the Netherlands
Tel: +31/(0)10/7043478
Fax: +31/(0)10/7043014
Web: http://www.erasmusmc.nl/biostatistiek/