[R] help with parsing multiple coxph() results

[Fredrik Lundgren]

Hao,

I'm not sure but you have specified your modell as tautology. The 
formula below should be enough:

survtest <- coxph(Surv(fup_interval, endpoint) ~ geneid, data = 
pcc.primary.stg.3.cox)

HTH
Fredrik
----- Original Message ----- 
From: "Hao Liu" <liuha at umdnj.edu>
To: <r-help at stat.math.ethz.ch>
Sent: Tuesday, January 17, 2006 7:47 PM
Subject: [R] help with parsing multiple coxph() results


> 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
>
>
>
> [[alternative HTML version deleted]]
>
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