[R] Help with correlation matrices, thresholding

[Drinniol]

Hello, I am new to R and have a problem I have had some trouble with.  

Basically I have a list of some 80000 genes or so with data points for
expression levels at various time points/conditions.  I also have subsets of
these, usually only a few hundred genes in size, known to be associated with
some biological process.

What I want to do is correlate the entire list with my subset and then
return out the gene names and correlations for correlations above a certain
threshold - the idea being that these would be good candidate genes to look
at more closely for possible interaction with said biological process.  

What functions should I use to correlate the subset to the whole set -
keeping in mind that I need to keep track of gene names in both sets?  And
how, then, from what I presume would be something like a 80000 x 200 sized
matrix would I extract gene pair correlations over a certain threshold?  It
would also probably be good if I could somehow remove the subset genes from
the whole gene list before computation so as to avoid useless 1
correlations.  

I'll keep trying on my own, but any help would be appreciated!

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