R help - Jan 2006 - 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
 
 

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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]]
>
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide! 
> http://www.R-project.org/posting-guide.html
>

Thanks for your reply, but I am not sure if I understand your reply right:
 
are you saying the "geneid" in  your post is a vector of all 22283
genes? I
want to do cox fit to each and everyone of the 22283 genes and need a way to
summarize it -- to do that, I need to know how to parse the result for each
coxph result.
 
Thanks
Hao

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