row correlations between two matrices

rowcors.R

rowCors = function(x, y)
{ 
	sqr = function(x) x*x
	if(!is.matrix(x)||!is.matrix(y)||any(dim(x)!=dim(y)))
	  stop("Please supply two matrices of equal size.")
	x   = sweep(x, 1, rowMeans(x))
	y   = sweep(y, 1, rowMeans(y))
	cor = rowSums(x*y) /  sqrt(rowSums(sqr(x))*rowSums(sqr(y)))
	return(cor)
}

# make two matrices each with 100 CpGs and 200 individuals
matrix1 <- matrix(rnorm(100*200), 100, 200)
matrix2 <- matrix(rnorm(100*200), 100, 200)

# Get the correlation of CpG1 in matrix1 against CpG1 in matrix2
# Get the correlation of CpG2 in matrix1 against CpG2 in matrix2
# Get the correlation of CpG3 in matrix1 against CpG3 in matrix2
# etc
rowCors(matrix1, matrix2)