search for: coxsnps

...g confused. It is not smart enough to match a new data frame that contains a numeric for sitenew to a fit that contained that variable as a factor. (Perhaps it should be smart enough to at least die gracefully -- but it's not). The simple solution is to not use factors. site1 <- 1*(coxsnps$sitenew==1) site2 <- 1*(coxsnps$sitenew==2) test1 <- coxph(Surv(time, censor) ~ snp1 + sex + site1 + site2 + gene + eth.self + strata(edu), data= coxsnps) output profile1 <- data.frame(snp1=c(0,1), site2=c(0,0), sex=c(0,0), site1=c(0,0), site2=c(0,0), geno=c(0,0...

...ose of the plot will be to visualise the effect of snp1, coded 0 and 1. In my Cox model I have stratified by one variable, edu, and so I know I will automatically get a separate curve for each strata. My problem is how to deal with the variable sitenew, which is a 3 level factor (coded 0,1,2). coxsnps$edu <- as.factor(coxsnps$edu) coxsnps$sitenew <- as.factor(coxsnps$sitenew) test1 <- coxph(Surv(time,censor) ~ snp1 + sex + sitenew + geno + eth_self + strata(edu), data=coxsnps) coef exp(coef) se(coef) z p snp1 -0.4324 0.649...