R: Estimates D' between multiple markers

dprfast {GenABEL} | R Documentation

## Estimates D' between multiple markers

### Description

Given a set of SNPs, computes a matrix of D'

### Usage

    dprfast(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 D' 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 D' and genetic coverage. Bioinformatics, 23: 252-254.

### See Also

`rhofast`

### Examples

    require(GenABEL.data)
    data(ge03d2)
    # D's using D'fast
    a <- dprfast(ge03d2,snps=c(1:10))
    ## Not run:
    library(genetics)
    # D's using package genetics
    b <- LD(as.genotype(ge03d2[,1:10]))$"D'"
    # see that the D's 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]