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

From: Dimitris Rizopoulos <d.rizopoulos_at_erasmusmc.nl>
Date: Sun, 13 Mar 2011 18:32:10 +0100

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/

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Received on Sun 13 Mar 2011 - 17:36:41 GMT

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