On Thu, Feb 23, 2012 at 3:24 PM, Bert Gunter <gunter.ber...@gene.com> wrote: > Use 1:n as an index. > > e.g. > sapply(1:n, function(i) cor(x[,i],y[,i]))
## sapply is a good solution (the only one I could think of too), but not always worth it: # for 100 x 1000 x <- data.frame(matrix(rnorm(100000),nc=1000)) y <- data.frame(matrix(rnorm(100000),nc=1000)) system.time(diag(cor(x,y))) # user system elapsed # 0.592 0.008 0.623 system.time(sapply(1:1000,function(i) cor(x[,i],y[,i]))) # user system elapsed # 0.384 0.000 0.412 # Great. but for 10 x 1000 x <- data.frame(matrix(rnorm(10000),nc=1000)) y <- data.frame(matrix(rnorm(10000),nc=1000)) system.time(diag(cor(x,y))) # user system elapsed # 0.256 0.008 0.279 system.time(sapply(1:1000,function(i) cor(x[,i],y[,i]))) # user system elapsed # 0.376 0.000 0.388 # or 100 x 100 system.time(diag(cor(x,y))) # user system elapsed # 0.016 0.000 0.014 system.time(sapply(1:100,function(i) cor(x[,i],y[,i]))) # user system elapsed # 0.036 0.000 0.036 # Not so great. Bottom line, as always, it depends. Cheers Elai > > -- Bert > > > > On Thu, Feb 23, 2012 at 2:10 PM, Sam Steingold <s...@gnu.org> wrote: >> suppose I have two sets of vectors: x1,x2,...,xN and y1,y2,...,yN. >> I want N correlations: cor(x1,y1), cor(x2,y2), ..., cor(xN,yN). >> my sets of vectors are arranged as data frames x & y (vector=column): >> >> x <- data.frame(a=rnorm(10),b=rnorm(10),c=rnorm(10)) >> y <- data.frame(d=rnorm(10),e=rnorm(10),f=rnorm(10)) >> >> cor(x,y) returns a _matrix_ of all pairwise correlations: >> >> cor(x,y) >> d e f >> a 0.2763696 -0.3523757 -0.373518870 >> b 0.5892742 -0.1969161 -0.007159589 >> c 0.3094301 0.1111997 -0.094970748 >> >> which is _not_ what I want. >> >> I want diag(cor(x,y)) but without the N^2 calculations. >> >> thanks. >> >> -- >> Sam Steingold (http://sds.podval.org/) on Ubuntu 11.10 (oneiric) X >> 11.0.11004000 >> http://www.childpsy.net/ http://iris.org.il http://americancensorship.org >> http://dhimmi.com http://www.PetitionOnline.com/tap12009/ >> http://jihadwatch.org >> Never argue with an idiot: he has more experience with idiotic arguments. >> >> ______________________________________________ >> 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. > > > > -- > > Bert Gunter > Genentech Nonclinical Biostatistics > > Internal Contact Info: > Phone: 467-7374 > Website: > http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm > > ______________________________________________ > 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-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.
