Description Usage Arguments Details Value Author(s) References See Also Examples

This function calculates measures of linkage disequilibrium between
pairs of SNPs. The two SNPs in each pair may both come from the same
`SnpMatrix`

object, or from two different `SnpMatrix`

objects. Statistics which can be calculated are the
log likelihood ratio, odds ratio, Yule's Q, covariance, D-prime,
R-squared, and R.

1 |

`x` |
An object of class |

`y` |
(Optional) Another object of the same class as |

`depth` |
When |

`stats` |
A character vector specifying the linkage disequilibrium measures to
be calculated. This should contain one or more of the strings: |

`symmetric` |
When no |

For each pair of SNPs, phased haplotype frequencies are first estimated
by maximum likelihood using the method described by Clayton and Leung
(2007). The arrays of chosen LD statistics are then calculated and
returned, either as
band matrices (when `y`

is not supplied), or as conventional
rectangular matrices (when `y`

is supplied). Band matrices are
stored in compressed form as objects of class `dsCMatrix`

(symmetric) or `dgCMatrix`

(upper triangular). These classes are
defined in the `"Matrix"`

package)

If only one LD statistic is requested, the function returns either a matrix or a compressed band matrix. If more than one LD statistic is requested, a list of such objects is returned

David Clayton [email protected]

Clayton and Leung (2007) *Human Heredity*, **64**:45-51,
(this paper is included in package documentation)

1 2 3 |

```
Loading required package: survival
Loading required package: Matrix
```

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