snp.cor: Correlations with columns of a snp.matrix
In chopsticks: The 'snp.matrix' and 'X.snp.matrix' Classes

Description Usage Arguments Details Value Note Author(s) See Also Examples

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.

1	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

xxt

# 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 eaxample to plot against chromosome position
loadings <- snp.cor(small, pc[,1:10])

Loading required package: survival
Warning message:
In methods:::bind_activation(TRUE) :
  methods:::bind_activation(TRUE) is deprecated;
 you should rather provide methods for cbind2() / rbind2()
Warning message:
In xxt(small, correct.for.missing = TRUE) :
  With correct.for.missing option set, result may not be a positive semi-definite matrix