Description Usage Arguments Details Value See Also Examples

This function produces (parametric or nonparametric) bootstrap estimates of
the IBD coefficients between two individuals. Both kappa and delta
coefficients are supported (see `ibdEstimate()`

).

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

`x` |
A |

`ids` |
A pair of ID labels. |

`param` |
Either NULL (default), "kappa" or "delta". (See below.) |

`kappa, delta` |
Probability vectors of length 3 (kappa) or 9 (delta).
Exactly one of |

`N` |
The number of simulations. |

`method` |
Either "parametric" (default) or "nonparametric". Abbreviations are allowed. see Details for more information about each method. |

`freqList` |
A list of probability vectors: The allele frequencies for each marker. |

`plot` |
A logical, only relevant for bootstraps of kappa. If TRUE, the bootstrap estimates are plotted in the IBD triangle. |

`seed` |
An integer seed for the random number generator (optional). |

The parameter `method`

controls how bootstrap estimates are obtained in each
replication.

If `method = "parametric"`

, new profiles for two individuals are simulated
from the input coefficients, followed by a re-estimation of the coefficients.

If `method = "nonparametric"`

, the original markers are sampled with
replacement, before the coefficients are re-estimated.

A data frame with `N`

rows containing the bootstrap estimates. The
last column (`dist`

) gives the euclidean distance to the original
coefficients, viewed as a point in R^3 (kappa) or R^9 (delta).

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 | ```
# Frequency list of 15 standard STR markers
freqList = NorwegianFrequencies[1:15]
# Number of bootstrap simulations (increase!)
N = 5
# Bootstrap estimates for kappa of full siblings
boot1 = ibdBootstrap(kappa = c(0.25, .5, .25), N = N, freqList = freqList)
boot1
# Mean deviation
mean(boot1$dist)
# Same, but with the 9 identity coefficients.
delta = c(0, 0, 0, 0, 0, 0, .25, .5, .25)
boot2 = ibdBootstrap(delta = delta, N = N, freqList = freqList)
# Mean deviation
mean(boot2$dist)
#### Non-parametric bootstrap.
# Requires `x` and `ids` to be provided
x = nuclearPed(2)
x = markerSim(x, ids = 3:4, N = 50, alleles = 1:10, seed = 123)
bootNP = ibdBootstrap(x, ids = 3:4, param = "kappa", method = "non", N = N)
# Parametric bootstrap can also be done with this syntax
bootP = ibdBootstrap(x, ids = 3:4, param = "kappa", method = "par", N = N)
``` |

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