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.

### See Also

`rhofast`

### Examples

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 1.6-7

Index]