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

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.

1 |

`x` |
An |

`y` |
An |

`uncertain` |
If |

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 [email protected]

1 2 3 4 5 6 7 8 9 | ```
# 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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