help with coxph() for multiple genes

classic Classic list List threaded Threaded
1 message Options
Reply | Threaded
Open this post in threaded view
|

help with coxph() for multiple genes

Hao Liu
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]]

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