[R] Correlation between 2 matrices but with subset of variables
A Ezhil
ezhil02 at yahoo.com
Sat Mar 10 01:54:07 CET 2012
Dear Peter,
Thank you very much.
Best regards,
Ezhil
--- On Fri, 3/9/12, Petr Savicky <savicky at cs.cas.cz> wrote:
> From: Petr Savicky <savicky at cs.cas.cz>
> Subject: Re: [R] Correlation between 2 matrices but with subset of variables
> To: r-help at r-project.org
> Date: Friday, March 9, 2012, 1:18 PM
> 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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