This function calculates Pearson correlation coefficients between columns of a
SnpMatrix and columns of an ordinary matrix. The two matrices
must have the same number of rows. All valid pairs are used in the
computation of each correlation coefficient.
An N by M
An N by P general matrix
This can be used together with
eigen to calculate standardized loadings in the principal
An M by P matrix of correlation coefficients
This version cannot handle X chromosomes
David Clayton [email protected]
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# make a SnpMatrix with a small number of rows data(testdata) small <- Autosomes[1:100,] # Calculate the X.X-transpose matrix xx <- xxt(small, correct.for.missing=TRUE) # Calculate the principal components pc <- eigen(xx, symmetric=TRUE)$vectors # Calculate the loadings in first 10 components */ loadings <- snp.cor(small, pc[,1:10])
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