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

Calculates the singlepoint log of the odds (LOD) scores of a pedigree for the specified markers, assuming a fixed recombination rate between the disease and each marker locus.

1 2 3 4 5 6 7 8 9 10 11 12 |

`x` |
A |

`aff` |
A vector naming the affected pedigree members, or a numeric vector
of length |

`model` |
A |

`rho` |
A number between 0 and 0.5 (inclusive); the hypothesised recombination ratio between the marker and the disease locus. |

`liability` |
NULL (default) or a vector of length |

`markers` |
A vector of marker names or indices referring to markers
attached to |

`maxOnly` |
a logical indicating whether only the maximum LOD score should be returned. By default this is always done if the number of markers is 1. |

`loopBreakers` |
A vector of ID labels indicating loop breakers. (Only relevant for inbred pedigrees.) |

`peelOrder` |
For internal use. |

`verbose` |
a logical: verbose output or not. |

The LOD score of a marker is defined as

*% LOD(ρ) = \log L(ρ)/L(0.5)*

where the
logarithms are base 10, and *L(ρ)* denotes the likelihood of the
observed marker genotypes given a recombination ratio *ρ* between the
marker and the disease locus.

The likelihoods are computed with the **pedprobr** package.

If the number of markers is 1, or if `maxOnly = TRUE`

, a single
number is returned.

Otherwise a `linkres`

object, which is basically a data frame with columns
`CHROM`

, `MARKER`

, `MB`

and `LOD`

.

Magnus Dehli Vigeland

linkres, `merlinLod()`

, `diseaseModel()`

, `lodPeaks()`

1 2 3 4 5 6 7 8 9 | ```
x = nuclearPed(2)
x = setMarkers(x, marker(x))
genotype(x, 1, c(1,2:4)) = 1:2
genotype(x, 1, 2) = 1
aff = c(2,1,2,2)
model = diseaseModel(model = "AD")
lod(x, aff, model)
``` |

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