[R] error: subscript out of bounds?
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$coef[4,5]))
}
write.table(test,result.txt,quote=F)
Thanks!
-CC
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Re: [R] ERROR: cannot allocate vector of size?
Hi! Thanks for your reply! After running the command below I am certain I am using a 64-bit R. I am running R through a linux cluster system where R is globally available for all users. I have asked the system administrators if they would update their version R but they are not receptive of making the change. If I must, I will try to install an updated version in my local directory. Though before I do that I want to make sure there are no other underlying issues I should consider. Could there be something else I need to look into? .Machine$sizeof.pointer [1] 8 Thank you! 2010/5/21 Uwe Ligges lig...@statistik.tu-dortmund.de At first, I'd try with an R version from 2010 rather than one from 2007. Next, I'd try to be sure to really have a 64-bit version of R rather than a 32 bit one which is what I suspect. Best, Uwe Ligges On 20.05.2010 20:10, Yesha Patel wrote: I've looked through all of the posts about this issue (and there are plenty!) but I am still unable to solve the error. ERROR: cannot allocate vector of size 455 Mb I am using R 2.6.2 - x86_64 on a Linux x86_64 Redhat cluster system. When I log in, based on the specs I provide [qsub -I -X -l arch=x86_64] I am randomly assigned to a x86_64 node. I am using package GenABEL. My data (~ 650,000 SNPs, 3,000 people) loads in okay and I am able to look at the data using basic commands [nids, nsnps, names(phdata)] The problem occurs when I try to run the extended analysis: xs- mlreg(GASurv(age,dm2)~sex,dta) ** 1) I have looked through the memory limits on R mem.limits() nsize vsize NANA 2) Code: gc() used (Mb) gc trigger (Mb) max used (Mb) Ncells 961605 51.41710298 91.4 1021138 54.6 Vcells 64524082 492.3 248794678 1898.2 68885474 525.6 gc(reset=TRUE) used (Mb) gc trigger (Mb) max used (Mb) Ncells 961119 51.41710298 91.4 961119 51.4 Vcells 64523417 492.3 199035742 1518.6 64523417 492.3 3) Linux Memory Allocation - Note: Max Memory Size, Virtual Memory Stack Size are all unlimited bash-3.2$ core file size (blocks, -c) 0 data seg size (kbytes, -d) unlimited scheduling priority (-e) 0 file size (blocks, -f) unlimited pending signals (-i) 31743 max locked memory (kbytes, -l) 32 max memory size (kbytes, -m) unlimited open files (-n) 32768 pipe size(512 bytes, -p) 8 POSIX message queues (bytes, -q) 819200 real-time priority (-r) 0 stack size (kbytes, -s) unlimited cpu time (seconds, -t) unlimited max user processes (-u) 31743 virtual memory (kbytes, -v) unlimited file locks (-x) unlimited 4) free -mt total used free sharedbuffers cached Mem: 3901 99 3802 0 1 24 -/+ buffers/cache: 73 3827 Swap: 1027 37990 Total:4929136 4792 5) ps -u USER PID %CPU %MEMVSZ RSS TTY STAT START TIME COMMAND xx 22352 0.0 0.0 65136 956 pts/0S03:09 0:00 -tcsh xx 22354 0.0 0.0 13496 1792 pts/0S03:09 0:00 /usr/sbin/pbs_m xx 22355 0.0 0.0 623260 pts/0S03:09 0:00 pbs_demux xx 29872 0.0 0.0 63736 920 pts/0R+ 09:45 0:00 ps -u ** Any solutions? Thank you! [[alternative HTML version deleted]] __ R-help@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. [[alternative HTML version deleted]] __ R-help@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.
[R] ERROR: cannot allocate vector of size?
I've looked through all of the posts about this issue (and there are plenty!) but I am still unable to solve the error. ERROR: cannot allocate vector of size 455 Mb I am using R 2.6.2 - x86_64 on a Linux x86_64 Redhat cluster system. When I log in, based on the specs I provide [qsub -I -X -l arch=x86_64] I am randomly assigned to a x86_64 node. I am using package GenABEL. My data (~ 650,000 SNPs, 3,000 people) loads in okay and I am able to look at the data using basic commands [nids, nsnps, names(phdata)] The problem occurs when I try to run the extended analysis: xs - mlreg(GASurv(age,dm2)~sex,dta) ** 1) I have looked through the memory limits on R mem.limits() nsize vsize NANA 2) Code: gc() used (Mb) gc trigger (Mb) max used (Mb) Ncells 961605 51.41710298 91.4 1021138 54.6 Vcells 64524082 492.3 248794678 1898.2 68885474 525.6 gc(reset=TRUE) used (Mb) gc trigger (Mb) max used (Mb) Ncells 961119 51.41710298 91.4 961119 51.4 Vcells 64523417 492.3 199035742 1518.6 64523417 492.3 3) Linux Memory Allocation - Note: Max Memory Size, Virtual Memory Stack Size are all unlimited bash-3.2$ core file size (blocks, -c) 0 data seg size (kbytes, -d) unlimited scheduling priority (-e) 0 file size (blocks, -f) unlimited pending signals (-i) 31743 max locked memory (kbytes, -l) 32 max memory size (kbytes, -m) unlimited open files (-n) 32768 pipe size(512 bytes, -p) 8 POSIX message queues (bytes, -q) 819200 real-time priority (-r) 0 stack size (kbytes, -s) unlimited cpu time (seconds, -t) unlimited max user processes (-u) 31743 virtual memory (kbytes, -v) unlimited file locks (-x) unlimited 4) free -mt total used free sharedbuffers cached Mem: 3901 99 3802 0 1 24 -/+ buffers/cache: 73 3827 Swap: 1027 37990 Total:4929136 4792 5) ps -u USER PID %CPU %MEMVSZ RSS TTY STAT START TIME COMMAND xx 22352 0.0 0.0 65136 956 pts/0S03:09 0:00 -tcsh xx 22354 0.0 0.0 13496 1792 pts/0S03:09 0:00 /usr/sbin/pbs_m xx 22355 0.0 0.0 623260 pts/0S03:09 0:00 pbs_demux xx 29872 0.0 0.0 63736 920 pts/0R+ 09:45 0:00 ps -u ** Any solutions? Thank you! [[alternative HTML version deleted]] __ R-help@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.
[R] GenABEL - problems with load.gwaa.data
Hi all! I am using GenABEL on R for GWAS analysis. I am having a couple of issues: First, I am having a problem reading files (.map, .ped, size 900Mb, using windows 32-bit) onto R in the convert.snp.ped statement. I am thinking this problem is likely due to the large size of the files my version of R is not able to handle them, since I can read in smaller files. Second, and the more precedent issue, is with the load.gwaa.data statement. It keeps giving me the error: more columns than column names. I have tried to read in the .dat file (and alternately the .csv file) without the header, that does not work. I have checked my data-set and there aren't any discernible columns that are missing. Here's my code: mix - load.gwaa.data (phe = Z:/.../CCF Pheno.csv, gen = pedmap-0.raw, force = T) Any help will be appreciated. Thanks! Euphie [[alternative HTML version deleted]] __ R-help@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.
