R: Estimates rho between multiple markers

rhofast {GenABEL} | R Documentation

## Estimates rho between multiple markers

### Description

Given a set of SNPs, computes a matrix of rho

### Usage

    rhofast(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

Rho is the measure of association described by N. Morton and A. Collins (see reference). The function is based on slightly modified code of Hao et al.

### Value

A (Nsnps X Nsnps) matrix giving rho values between a pairs of SNPs above the diagonal and Kij below the diagonal.

### Author(s)

Yurii Aulchenko

### References

Collins A, Morton NE. (1998) Mapping a disease locus by allelic association. PNAS, 17:1741-1745.

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

### See Also

`r2fast`

### Examples

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