As Petr suggests, the dist() function will do much of the work for you. 
For example ...
# example matrix of data
nsamples <- 40
nreadings <- 460000
dat <- matrix(runif(nsamples*nreadings), nrow=nsamples)
# Euclidean distance between the ROWS of dat
distance <- dist(dat)

Jean


JenniferH <jenachobbs@gmail.com> wrote on 08/01/2012 04:42:48 AM:
> 
> Hello everyone.  Like others on this list, I'm new to R, and really not 
much
> of a programmer, so please excuse any obtuse questions!  I'm trying to
> repeat a function across all possible combinations of vectors in a data
> frame.  I'd hugely appreciate any advice!
> 
> Here's what I'm doing:
> 
> I have some data: 40 samples, ~460 000 different readings between 1 and 
0
> for each sample.  I would like to make R spit out a matrix of distances
> between the samples.  So far, I have made a function to calculate the
> distance between any two samples:
> 
> DistanceCalc<-function(x,y){#x and y are both vectors - the entire 
reading
> set for sample x and
> #sample y, respectively
>   distance<-sqrt(sum((x-y).^2))
>   distanceCorrected<-distance/sqrt(length(x))#to force the maximum 
possible
> value to =1
>   print(distanceCorrected)
> }
> 
> The next thing I want to do is to make this function run to compare all
> possible combinations of my samples (1vs1, 1vs2, 1vs3...2vs1, 2vs2 etc). 
 In
> python, the only other programming language I have ever used, I would 
just
> use a "for" loop.  I have asked the internet how to do this, but the
> overwhelming response seems to be "you don't want to do it like that - 
use
> the 'apply' functions".  I've tried to use the apply functions, but I 
tend
> to find that I can only give my DistanceCalc function a single vector (I 
can
> tell it where to find x, but not where to find y, or vice versa).  I've 
also
> found the 'by' and the 'outer' functions, but I'm likewise failing at 
making
> those work, e.g.
> 
> > 
distancetable<-outer(DataWithoutBlanks,DataWithoutBlanks,FUN=DistanceCalc)
> Error in x - y : non-numeric argument to binary operator
> 
> I think this may be because my data has headers and the function is 
trying
> to calculate the difference between the names of my samples, but I don't
> know how to correct this.
> 
> Would really appreciate your help!
> 
> Jen

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