GenABEL (version 1.8-0)

rhofast: Estimates rho between multiple markers

Description

Given a set of SNPs, computes a matrix of rho

Usage

rhofast(data, snpsubset, idsubset)

Arguments

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.

Value

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

Details

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.

References

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.

See Also

r2fast

Examples

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)