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)
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$coef[4,5]))
}
write.table(test,"result.txt",quote=F)
Thanks!
-CC
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You need to learn how to debug your program. When the error occurs, look at the value of the indices in the offending statement -- you will find that the problem is subscript out of bounds. Put the following statement in your code: options(error=utils::recover) and then do ?browser to learn how to use the browser for debugging. On Mon, Jun 14, 2010 at 6:48 PM, Yesha Patel <turtysmail at gmail.com> wrote:> Hi all, > > I want to get results for cox proportional hazards on SNP data. I'm trying > to get HRs, CI's, & p-values for each individual SNP - this is represented > by cov[,i]. When I run my code, I get the following error: subscript out of > bounds. I don't know why I am getting this error. > > I have looked through the R logs, but nothing that has been previously > suggested has helped so far. What am I doing wrong? > > DS3 = time variable, S3 = censor/event variable, cov = my dataset, which is > in a data.frame format: > > ********************************************************* > CODE: > > test<-NULL > bb=names(cov) > col = dim(cov)[2] > for(i in 19:col) > ?{ > mod=coxph(Surv(cov$DS3,cov$S3)~cov[,i]+AGE+sex,data=cov) > aa<-summary(mod) > ?test<-rbind(test,c(bb[i],aa$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])) > } > write.table(test,"result.txt",quote=F) > > > Thanks! > -CC > > ? ? ? ?[[alternative HTML version deleted]] > > ______________________________________________ > R-help at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. >-- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem that you are trying to solve?
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 > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code.David Winsemius, MD West Hartford, CT