pair.result.ld.snp: Function to calculate the pairwise D', $r^2$, LOD of a pair...

In chopsticks: The 'snp.matrix' and 'X.snp.matrix' Classes

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 [e-mail]

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)

chopsticks documentation built on Nov. 8, 2020, 7:51 p.m.