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

Estimates the probability that all subjects in a set of pedigree members share a rare variant given that it occured in any of them by performing a Monte Carlo simulation of the transmission of the genotypes of the variant from the founders down the pedigree.

1 2 | ```
GeneDropSim.fn(trio.list, id, dt.vec, fd.indices, carriers=dt.vec, n = 1e3,
k = 10, nf = 1)
``` |

`trio.list` |
a list of trio objects encoding the pedigree structure. |

`id` |
a vector of identifiers of the pedigree members. |

`dt.vec` |
a vector of identifiers of the subset of pedigree members for which to estimate the sharing probability. Must be a subset of the |

`fd.indices` |
a vector of the indices of the founders of the pedigree. |

`carriers` |
optional character vector of subjects carrying the rare variant among all final descendants. If null, all final descendants are assumed to carry the rare variant. |

`n` |
minimal number of gene dropping replicates where the rare variant occurs in at least one member of |

`k` |
this number times |

`nf` |
number of founders introducing the rare variant into the pedigree. |

The transmission of the RV down the pedigree from the `nf`

founders introducing it is simulated according to Mendel's laws. The events that the variant was observed in any of the subjects from `dt.vec`

and in all subjects included in `carriers`

are then recorded. The simulation continues until the number of replicates where the RV was observed in any of the subjects from `dt.vec`

reaches `n`

or the number of replicates reaches `k n`

. The RV sharing probability is then estimated as the number of replicates where the RV was observed in all subjects included in `carriers`

over `n`

(or the number of replicates where the RV was observed in any of the subjects when `k n`

replicates are reached).

Estimate of the probability that all subjects in a subset of pedigree members share a rare variant given that it occured in any of them

Samuel G. Younkin <[email protected]> and Alexandre Bureau <[email protected]>

Bureau, A., Younkin, S., Parker, M.M., Bailey-Wilson, J.E., Marazita, M.L., Murray, J.C., Mangold, E., Albacha-Hejazi, H., Beaty, T.H. and Ruczinski, I. (2014) Inferring rare disease risk variants based on exact probabilities of sharing by multiple affected relatives. Bioinformatics, 30(15): 2189-96, doi:10.1093/bioinformatics/btu198.

`ped2trio, GeneDropSim.allsubsets.fn, GeneDropSimExcessSharing.fn`

1 2 3 4 5 6 7 8 9 |

syounkin/RVsharing documentation built on May 31, 2019, 12:47 a.m.

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