Estimates r2 between multiple markers

r2fast.old {GenABEL}R Documentation

Estimates r2 between multiple markers

Description

Given a set of SNPs, computes a matrix of r2

Usage

r2fast.old(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.

Details

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

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

Author(s)

Yurii Aulchenko

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

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)

[Package GenABEL version 1.6-7 Index]