On Jun 14, 2010, at 6:48 PM, Yesha Patel wrote:
Hi all,
I want to get results for cox proportional hazards on SNP data. I'm
trying
to get HRs, CI's, & p-values for each individual SNP - this is
represented
by cov[,i]. When I run my code, I get the following error: subscript
out of
bounds. I don't know why I am getting this error.
I have looked through the R logs, but nothing that has been previously
suggested has helped so far. What am I doing wrong?
DS3 = time variable, S3 = censor/event variable, cov = my dataset,
which is
in a data.frame format:
*********************************************************
CODE:
test<-NULL
bb=names(cov)
col = dim(cov)[2]
for(i in 19:col)
{
mod=coxph(Surv(cov$DS3,cov$S3)~cov[,i]+AGE+sex,data=cov)
aa<-summary(mod)
# Consider:
test <-rbind( test, c( nrow(aa$coef), nrow(aa$conf.int) ) )
#test<-rbind(test,c(bb[i],aa$coef[1,1],aa$coef[1,3],aa$coef[1,5],aa
$conf.int
#[1,1],aa$conf.int[1,3],aa$conf.int
#[1,4],aa$coef[2,5],aa$coef[3,5],aa$coef[4,5]))
}
#
c(min(test[ , 1] ), min(test[ ,2] ) )
#write.table(test,"result.txt",quote=F)
# Compare to your indices.
Thanks!
-CC
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