HI Wudd Wudd -- not really answering your question, but it might pay
to refactor some of your R code first. For instance
for(j in 2:nrow(ranklist)){
phit <- sum(rep(1/Ns, sum(ranklist[1:j,2]==1)))
pmiss <- sum(rep(1/(N-Ns), sum(ranklist[1:j,2]==0)))
if((phit-pmiss)>score[i]) score[i] <- phit - pmiss
}
might be replaced (you'd better check, I'm not sure I have your logic
correct) by
phit <- (cumsum(ranklist[,2]==1) / Ns)[-1]
pmiss <- (cumsum(ranklist[,2]==0) / (N - Ns))[-1]
pmax <- max(phit - pmiss)
if (pmax > score[i]) score[i] <- pmax
These should be much faster than your loop. Your earlier 'apply' might
also be replaced by rowMeans, etc. I think, and once simplified to
that level further higher-level reorganizations might be possible.
Hope that helps
Martin
wudd wudd <wudds...@gmail.com> writes:
> Hi guys,
> I want to transfer the following code from R into .Call compatible form. How
> can i do that?
>
> Thanks!!!
>
> INT sim;
> for(i in 1:sim){
> if(i>2) genemat <- genemat[,sample(1:ncol(genemat))]
> ranklist[,1] <- apply(genemat, 1, function(x){
> (mean(x[cols]) -
> mean(x[-cols]))/sd(x)})
> ranklist <- ranklist[order(ranklist[,1]),]
> if(ranklist[1,2]==1) score[i] <- 1/Ns
> if(ranklist[1,2]==0) score[i] <- -(1/(N-Ns))
> for(j in 2:nrow(ranklist)){
> phit <- sum(rep(1/Ns, sum(ranklist[1:j,2]==1)))
> pmiss <- sum(rep(1/(N-Ns), sum(ranklist[1:j,2]==0)))
> if((phit-pmiss)>score[i]) score[i] <- phit - pmiss
> }
> }
>
> I tried a little bit, but not enough knowledge in C.
> #include <stdio.h>
> #include <R.h>
> #include <Rdefines.h>
> #include <math.h>
> SEXP ESscore(SEXP Rgeneset, SEXP Rgenemat, SEXP Rranklist, SEXP sim)
> {
> int nc = ncols(Rgenemat);
> double *geneset = NUMERIC_DATA(Rgeneset);
> double *genemat = NUMERIC_DATA(Rgenemat);
>
> SEXP Rscore;
> PROTECT(Rscore=NEW_NUMERIC(sim));
> double *score = NUMERIC_DATA(Rscore);
>
> for(i=1; i<=sim; i++){
> if(i>2) {genemat <- genemat[,sample(1:nc)];}
> for(k=1; k<nc )
>
> }
>
> }
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
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> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
--
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
Location: Arnold Building M1 B861
Phone: (206) 667-2793
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