pair.result.ld.snp {chopsticks} | R Documentation

## Function to calculate the pairwise D', $r^2$, LOD of a pair of specified SNPs

### Description

`pair.result.ld.snp.Rd` calculates the pairwise D', $r^2$, LOD of a pair of specified SNPs in a `snp.matrix` object. This is used mainly for debugging.

### Usage

    pair.result.ld.snp(snpdata, loc.snpA, loc.snpB)

### Arguments

`snpdata` | An object of `snp.matrix` class with M samples of N snps
`loc.snpA` | index of the first snp; should be between 1 and N
`loc.snpB` | index of the second snp; should be between 1 and N

### Value

Returns nothing. Results are displayed in stdout/console.

### Note

Not really recommended for daily usage; the result isn't saved anywhere and this routine is primarily for debugging the details and correctness of the calculation.

### Author(s)

Hin-Tak Leung htl10@users.sourceforge.net

### References

Clayton, D.G. and Leung, Hin-Tak (2007) An R package for analysis of whole-genome association studies. Human Heredity 64:45-51.
GSL (GNU Scientific Library) http://www.gnu.org/software/gsl/

### See Also

`snp.matrix-class`

### Examples

    data(testdata)
    pair.result.ld.snp(Autosomes, 1, 2)

[Package chopsticks version 1.48.0 Index]