rhofast: Estimates rho between multiple markers
In GenABEL: genome-wide SNP association analysis

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

Given a set of SNPs, computes a matrix of rho

1	rhofast(data, snpsubset, idsubset)

`data`	object of `snp.data-class`
`snpsubset`	Index, character or logical vector with subset of SNPs to run analysis on. If missing, all SNPs from `data` are used for analysis.
`idsubset`	Index, character or logical vector with subset of IDs to run analysis on. If missing, all people from `data` are used for analysis.

Rho is the measure of association described by N. Morton and A. Collins (see reference). The function is based on slightly modified code of Hao et al.

A (Nsnps X Nsnps) matrix giving rho values between a pairs of SNPs above the diagonal and Kij below the diagonal.

Yurii Aulchenko

Collins A, Morton NE. (1998) Mapping a disease locus by allelic association. PNAS, 17:1741-1745.

Hao K, Di X, Cawley S. (2006) LdCompare: rapid computation of single- and multiple-marker rho and genetic coverage. Bioinformatics, 23: 252-254.

r2fast

require(GenABEL.data)
data(ge03d2)
# rhos using rhofast
a <- rhofast(ge03d2,snps=c(1:10))
## Not run: 
library(genetics)
# rhos using package genetics
b <- LD(as.genotype(ge03d2[,1:10]))$"R^2"
# see that the rhos are not exactly the same
cor(a[upper.tri(a)],b[upper.tri(b)])
plot(a[upper.tri(a)],b[upper.tri(b)])

## End(Not run)