R: 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.

Examples

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)

[Package GenABEL version 1.8-0 Index]