Question

I did coxph for my data and get result like this:

> z
Call:
coxph(formula = Surv(Years, Event) ~ y, data = x)


    coef exp(coef) se(coef)     z   p
y 0.0714      1.07    0.288 0.248 0.8


Likelihood ratio test=0.06  on 1 df, p=0.804  n= 65, number of events= 49 

I just want to save

y 0.0714      1.07    0.288 0.248 0.8

into a file. Because I do permutation and generate 1000 z.

I want to save them into a text file like this:

fin -0.3794 0.684 0.1914 -1.983 0.0470
age -0.0574 0.944 0.0220 -2.611 0.0090
race 0.3139 1.369 0.3080 1.019 0.3100
wexp -0.1498 0.861 0.2122 -0.706 0.4800
mar -0.4337 0.648 0.3819 -1.136 0.2600
paro -0.0849 0.919 0.1958 -0.434 0.6600

Anyone can help?

Thanks!

Answer 1

The coefficients are easily accessed by

summary(z)[['coefficients']]

and the confidence interval information by

summary(z)[['conf.int']]

To find out what the components of a summary.coxph object

str(summary(z))

My advice would be to create a list of your permutations

data_list <- list(data_1, ...., data_1000)

Then call

lots_models <- lapply(data_list, coxph, formula = Surv(Years, Event) ~ y)

Which creates a list of models

You can create the summaries by

lots_summaries <- lapply(lots_models, summary)

Extract the coefficients

all_coefficients <- lapply(lots_summaries, '[[', 'coefficients')
all_conf.int     <- lapply(lots_summaries, '[[', 'conf.int')

Add a permutation id column (if you want)

all_coefs_id <- lapply(seq_along(data_list), 
   function(i) cbind(all_coefficients[[i]],i))
all_ci_id <- lapply(seq_along(data_list), 
   function(i) cbind(all_conf.int[[i]],i))

Then combine into a data.frame

all_coefs_df <- do.call(rbind, all_coefs_id)
all_ci_df <- do.call(rbind, all_ci_id)

Which you than then save as a text file