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

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)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(chopsticks)
Loading required package: survival
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/chopsticks/pair.result.ld.snp.Rd_%03d_medium.png", width=480, height=480)
> ### Name: pair.result.ld.snp
> ### Title: Function to calculate the pairwise D', $r^2$, LOD of a pair of
> ###   specified SNPs
> ### Aliases: pair.result.ld.snp
> ### Keywords: htest models dplot
> 
> ### ** Examples
> 
> data(testdata)
> pair.result.ld.snp(Autosomes, 1, 2)
Information: samples = 400, snps = 9445
 ii = 1, jj = 2
 146	187	63	145.088161	189.219144	61.693325
 1	0	0	0.604534	0.394207	0.000000
 0	0	0	0.000630	0.000000	0.000000
d' = 1.000000 , r^2 = 0.000821, lod= 0.217854
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>