snp.cor {snpMatrix} | R Documentation |
This function calculates Pearson correlation coefficients between columns of a
snp.matrix
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.
snp.cor(x, y)
x |
An N by M snp.matrix |
y |
An N by P general matrix |
This can be used together with xxt
and
eigen
to calculate standardized loadings in the principal
components
An M by P matrix of correlation coefficients
This version cannot handle X chromosomes
David Clayton david.clayton@cimr.cam.ac.uk
# make a snp.matrix 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, # for example to plot against chromosome position loadings <- snp.cor(small, pc[,1:10])