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Choices from a matrix

If I understand you correctly, here's one way based on expand.grid().

I is just an index set, and so all you really need to do is generate your
2^k rows from the part of the matrix you're using in the right places via
replacement:  

e.g. newX<-matrix(0, ncol=ncol(X),nrow=2^length(I))
newX[,I]<-expand.grid(as.list(as.data.frame(X[,I]))) 


N.B. I tried to do the this without the explicit as.list() cast, but got an
error message. I would have thought that expand.grid should have recognized
that a data.frame IS a list without the cast.

-- Bert Gunter
Genentech Non-Clinical Statistics
South San Francisco, CA
 
"The business of the statistician is to catalyze the scientific learning
process."  - George E. P. Box