View source: R/estimate_time_phased.R

Calculates the time since admixture, given unphased ancestry data.

1 2 3 | ```
estimate_time_phased(local_anc_matrix, locations, pop_size,
freq_ancestor_1, lower_lim = 2, upper_lim = 1000,
optim_pop_size = FALSE, verbose = FALSE)
``` |

`local_anc_matrix` |
Local_anc can be provided as either matrix with two columns, where the first column represents ancestry on chromosome 1, and the second column represents ancestry on chromosome 2. Ancestry labels used should be [0, 1], where 0 indicates the first ancestor, and 1 indicates the second ancestor. Alternatively, the user can provide a vector using labels indicating whether at the specific marker, the focal individual is homozygous for the first ancestor (label = 1), homozygous for the second ancestor (label = 2), heterozygous [0,1] (label = 3) or heterozygous [1, 0] (label = 4). |

`locations` |
locations of the used markers (in Morgan) |

`pop_size` |
population size |

`freq_ancestor_1` |
Frequency of ancestor 1 at t = 0 |

`lower_lim` |
lower limit of the optimization algorithm. Increase if the expected admixture time is relatively ancient |

`upper_lim` |
upper limit of hte optimization algorithm. If set too large, recent admixture events can be overlooked - best to set as low as possible. |

`optim_pop_size` |
If TRUE, population size is also optimized. Starting point of the optimizaton will then be on the given population size, and half the maximum time. |

`verbose` |
display intermediate output? Default = FALSE |

thijsjanzen/junctions documentation built on Sept. 12, 2019, 5:47 p.m.

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