R: Estimates r2 between multiple markers

r2fast {GenABEL} | R Documentation

## 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.

### 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

    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)

[Package GenABEL version 1.8-0 Index]