[R] help with parsing multiple coxph() results

From: Hao Liu <liuha_at_umdnj.edu>
Date: Wed 18 Jan 2006 - 05:47:18 EST


Dear All:  

I have a question on using coxph for multiple genes:  

I have written code to loop through all 22283 genes in the Hgu-133A and apply coxph on survival data.  

However, I don't know how to work with the result for each gene:  

survtest<-coxph(Surv(pcc.primary.stg.3.cox[,'fup_interval'],pcc.primary.stg. 3.cox[,'endpoint'])~pcc.primary.stg.3.cox[,'geneid'],pcc.primary.stg.3.cox)  

each time I tried to look at what is in survtest it gives me this:  




coxph(formula = Surv(pcc.primary.stg.3.cox[, "fup_interval"],

    pcc.primary.stg.3.cox[, "endpoint"]) ~ pcc.primary.stg.3.cox[,     "208181_at"], data = pcc.primary.stg.3.cox)  

                                      coef exp(coef) se(coef)     z      p
pcc.primary.stg.3.cox[, "208181_at"] -1.87     0.154    0.688 -2.72 0.0065
 

Likelihood ratio test=8.56 on 1 df, p=0.00343 n= 48



 

What I wanted to do is to use a matrix to store each "survtest" result, but it seems to me there is no data
structure in R to store the result of coxph into a matrix. I got the following code to calculate a P value
based on "survtest"



z<-survtest$coefficients/sqrt(surv$var)
p<-2*(1-pnorm(abs(z)))  

then, what is the P value thus calculated?



The question I have are:  
  1. How do I access different parts of coxph result?
  2. Is there a way to store multiple coxph results into a data structure that can be efficiently accessed?
  3. if I find a list of genes I am interested, are there efficient to plot all of them based on the survial data?

Thanks
Hao Liu, Ph. D    

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