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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