snp.cor {snpStats} | R Documentation

## Correlations with columns of a SnpMatrix

### Description

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.

### Usage

    snp.cor(x, y, uncertain = FALSE)

### Arguments

`x` | An N by M `SnpMatrix`
`y` | An N by P general matrix
`uncertain` | If `TRUE`, uncertain genotypes are replaced by posterior expectations. Otherwise these are treated as missing values

### Details

This can be used together with `xxt` and `eigen` to calculate standardized loadings in the principal components

### Value

An M by P matrix of correlation coefficients

### Note

This version cannot handle X chromosomes

### Author(s)

David Clayton dc208@cam.ac.uk

### See Also

`xxt`

### Examples

    # 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])

[Package snpStats version 1.30.0 Index]