[R] Help with correlation matrices, thresholding
drinniol at gmail.com
Mon Jul 16 22:55:29 CEST 2012
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
I'll keep trying on my own, but any help would be appreciated!
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