help with coxph() for multiple genes

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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:




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"





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?



Hao Liu, Ph. D

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