I have a large correlation matrix that I'm trying to convert to a list of
every connection (edge) between every two nodes with its accompanying
correlation value (for Cytoscape). I figured out how to do this and to
remove the connections that nodes have to themselves but I can't figure out
how to get rid of the duplicate pairs (e.g. the edge b-a is a duplicate of
a-b).
NodesRow<-rep(c("a","b","c"),each=3)
NodesCol<-rep(c("a","b","c"),times=3)
Corr<-c(1,.8,.4,.8,1,.3,.4,.3,1)
data<-data.frame(NodesRow,NodesCol,Corr)
# above is what my node and edge dataframe looks like
data2<-subset(data,data[,1]!=data[,2])
# above is how I clear out connections nodes have to themselves
Thanks for any clues of a better way to do this!
Matt
Matthew DiLeo, Ph.D.
Postdoctoral Associate
Boyce Thompson Institute for Plant Research
Robert W. Holley Center, Tower Road, Ithaca
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