On Thu, Mar 08, 2012 at 03:57:06PM -0800, A Ezhil wrote:
> Dear All,
> I have two matrices A (40 x 732) and B (40 x 1230) and would like to
> calculate correlation between them. ?I can use: cor(A,B, method="pearson") to
> calculate correlation between all possible pairs. But the issue is that there
> is one-many specific mappings between A and B and I just need to calculate
> correlations for those pairs (not all). Some variables in A (proteins, say
> p1) have more than 3 (or 2 or 1) corresponding mapping in B (mRNA, say,
> m1,m2,m3) and I would like calculate correlations between p1-m1, p1-m2, and
> p1-m3 and then for the second variable p2 etc.?
> I have the mapping information in another file (annotation file). Could you
> please suggest me how to do that?
Hi.
Try the following.
1. Create some simple data
X <- matrix(rnorm(15), nrow=5, ncol=3)
Y <- matrix(rnorm(25), nrow=5, ncol=5)
2. Choose a table of pairs of columns, for which the correlation
should be computed, and expand the matrices.
ind <- rbind(
c(1, 1),
c(1, 2),
c(2, 2),
c(3, 3),
c(3, 4),
c(3, 5))
X1 <- X[, ind[, 1]]
Y1 <- Y[, ind[, 2]]
3. Compute the correlations between X1[, i] and Y1[, i] and
compare to the diagonal of cor(X1, Y1)
parallel.cor <- function(X, Y)
{
X <- sweep(X, 2, colMeans(X))
Y <- sweep(Y, 2, colMeans(Y))
colSums(X*Y)/sqrt(colSums(X^2)*colSums(Y^2))
}
out <- parallel.cor(X1, Y1)
verif <- diag(cor(X1, Y1))
all.equal(out, verif)
[1] TRUE
Hope this helps.
Petr Savicky.
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