Hi Jim,
This is genotype data of 170 samples. I selected subsets of SNP
optimized for different types of germplasm. So it is a matrix with 170
rows and 1536, 384 or 96 columns of binary data (0, 1). I have 14 of
such matrices in a list.
x <- list()
for (i in 1:14) {
set.seed(i)
x[[i]] <- matrix(sample(rep(c(1,0), 1000000), 1536*170), nrow = 170,
ncol = 1536)
}
Thanks,
Marc.
jim holtman wrote:
I have no idea of what your data looks like, so using random numbers
and only going for nr=1, after about a minute I stopped it. Here is
what Rprof showed:
/cygdrive/c/perf: perl c:/perf/bin/readRprof.pl Rprof.out 1
0 75.8 root
1. 75.7 sapply
2. . 75.7 lapply
3. . . 75.7 FUN
4. . . . 75.6 as.dist
5. . . . . 75.6 distance
6. . . . . . 75.6 distance.default
7. . . . . . . 75.4 apply
8. . . . . . . . 73.8 FUN
9. . . . . . . . . 73.8 switch
10. . . . . . . . . . 73.8 apply
11. . . . . . . . . . . 63.4 FUN
12. . . . . . . . . . . . 6.6 !
12. . . . . . . . . . . . 2.8 -
12. . . . . . . . . . . . 2.5 any
12. . . . . . . . . . . . 2.2 /
12. . . . . . . . . . . . 1.7 sum
12. . . . . . . . . . . . 1.6 *
11. . . . . . . . . . . 2.3 aperm
11. . . . . . . . . . . 1.0 unlist
8. . . . . . . . 1.5 join
This says almost all the time is in the 'distance' function. Try
running your data with 'nr' very small and see what happens.
On Tue, Jun 10, 2008 at 4:49 AM, Marc <[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>> wrote:
Hi,
I have the following function that I want to apply to a list of 14
matrices (1536 x 170) of binary data:
DRes <- function(x, nr = 10000, metric = "mixed", ...) {
require(analogue)
require(ade4)
m <- c()
for (i in 1:nr) {
set.seed(i)
x1 <- x[, sample(dimnames(x)[[2]], length(x[1,])/2)]
x2 <- x[, !dimnames(x)[[2]] %in% dimnames(x1)[[2]]]
d1 <- as.dist(distance(as.data.frame(x1), method = metric))
d2 <- as.dist(distance(as.data.frame(x2), method = metric))
m[i] <- mantel.rtest(d1, d2, ...)$obs
mean <- mean(m)
std <- sd(m)
res <- list(mean = mean, std = std)
}
return(res)
}
bias.dres <- sapply(bias, DRes)
I run this code and after 3 hours is still running. I am on
Windows XP and this is my sessionInfo()
> sessionInfo()
R version 2.7.0 Patched (2008-05-02 r45580)
i386-pc-mingw32
locale:
LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United
Kingdom.1252;LC_MONETARY=English_United
Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods
base
other attached packages:
[1] analogue_0.5-1 vegan_1.11-4 ade4_1.4-7
Any help will be very much appreciated.
Marc.
______________________________________________
R-help@r-project.org <mailto: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
<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 you are trying to solve?
______________________________________________
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.
