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

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 1.6-7 Index]