I'm using survminer to try to create a survival formula for a phenotype data set.
library("survival", "survminer") data <- read.csv(file = "Study.cleaned.csv", header = TRUE) basic.cox <- coxph(formula = Surv(Observation_time, Event_Detected) ~ Patient_Age + Sex+BMI, data = data) basic.assump <- cox.zph(basic.cox) sink('/home/varieties/variables.tsv') print(basic.assump) sink()
This produces a file that looks like this:
rho chisq p A 0.00477 0.0987 0.7534 B -0.02352 2.5383 0.1111 C 0.02513 3.2104 0.0732 GLOBAL NA 5.6162 0.1319
I have tried about 2,000 different combinations of each factor
L by summing them , e.g.
A+B+D+E... etc. but the problem is that none of the summaries have all p-values being < 0.05, which is a requirement of the study.
Also, some times factors will split, and I don't know why. The output file will look like this:
C<100 0.207766 9.59e-09 0.999922 C<50 0.188145 2.07e-08 0.999885 C<69 0.124370 9.49e-09 0.999922 C>325 0.138520 1.05e-08 0.999918 C100 0.004437 9.01e-02 0.764040 C100.0 0.189391 1.14e-08 0.999915 C101 -0.012151 6.76e-01 0.410877...
and I don't know why it's splitting like this.
I have two questions:
1. How can I determine a formula that will have all p-values < 0.05?
2. Why do some factors split like
C did in the example above?