Hi all,

I'm new to R, so needless to say I have a couple questions (which I hope 
I haven't missed through the documentation).
I have several files in lower triangular matrix form. For each of these 
matrices, I want to perform some form of hierarchical clustering on each 
matrix and capture the output of the clustering.

The first problem I run into is actually loading the matrix file into R. 
I've attempted using the read.table function but to no avail. What is 
the best way to read in a matrix?
    Note: matrices are in a form like so, a space between each value, 
then a newline There is also a diagonal of 0's stripped out. (Matrices 
are the output of RNAdistance if that's helpful)
    Let's say its stored in a file called 'rtest'          
                21
                34 55
                55 34 21
                27 10 61 44
                59 42 25 8 40
                61 44 27 10 34 6
                73 64 57 48 66 44 50
                78 69 62 53 71 49 55 5
                77 68 103 94 70 94 96 88 89
                77 68 103 94 70 90 96 84 85 10
                31 24 53 46 30 50 52 72 73 74 74

Second, I've searched through the web and it seems hclust 
<http://www.maths.lth.se/help/R/.R/library/mva/html/hclust.html> is the 
appropriate function From what I can tell from here 
<http://stat.ethz.ch/R-manual/R-devel/library/stats/html/dist.html> the 
above matrix should be a valid format (even without the 0s), but 
confirmation would be nice. And with hclust, does this produce a tree 
with the output, or would that be the plclust function? I haven't been 
able to experiment with this because of my inability to do accomplish 
the previous question.

And last, I want to be able to run R on many different files of the same 
matrix type. Is it possible to write a (Python) script run through the 
appropriate tasks and save the visual output as a postscript file?

Thanks in advance
- Mike Schuler




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