r2fast.old: Estimates r2 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 r2

1	r2fast.old(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.

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

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

Yurii Aulchenko

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

rhofast

require(GenABEL.data)
data(ge03d2)
# r2s using r2fast.old
a <- r2fast.old(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)