GenABEL (version 1.8-0)

r2fast: Estimates r2 between multiple markers

Description

Given a set of SNPs, computes a matrix of r2

Usage

r2fast(data, snpsubset, cross.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.

cross.snpsubset

Parameter allowing parallel implementation. Not to be used normally. If supplied together with snpsubset, the r2 for all pairs between snpsubset and cross.snpsubset computed.

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 r2 values between a pairs of SNPs above the diagonal and number of SNP genotype measured for both SNPs below the diagonal

Details

The function is based on slightly modified code of Hao et al.

References

Hao K, Di X, Cawley S. (2006) LdCompare: rapid computation of single- and multiple-marker r2 and genetic coverage. Bioinformatics, 23: 252-254.

See Also

rhofast

Examples

require(GenABEL.data)
data(ge03d2)
# r2s using r2fast
a <- r2fast(ge03d2,snps=c(1:10))
## Not run: 
# library(genetics)
# # r2s using package genetics
# b <- LD(as.genotype(ge03d2[,1:10]))$"R^2"
# # see that the r2s 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)