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

View source: R/HWEImportSamp.R

Importance sampling to calculate the normalizing constant under the single *f* model. Two proposals are available, either sampling from the prior or sampling from a normal distribution whose mean vector and variance-covariance matrix must be specified. The latter may be taken from an MCMC analysis using, for example, WinBUGS. In all cases the likelihood is multinomial and the prior is Dirichlet on the allele frequencies, and normal on *λ* where *λ=\log(f-f_{\min})/(1-f))*. See Weir (1996) for a description of HWE and different models/parameterizations.

1 2 3 |

`nsim` |
the number of points to sample to calculate the estimate. |

`nvec` |
vector of genotype frequencies in the order |

`ischoice` |
choice of importance sampling proposal, =1 gives a normal distribution with mean and variance that must be specified (as |

`lambdamu` |
the mean of the prior for |

`lambdasd` |
the variance of the prior for |

`alpha` |
the vector of |

`gmu` |
the mean of the importance sampling proposal, of length |

`gsigma` |
the variance of the importance sampling proposal, a matrix of dimension |

`PrnH1` |
the estimate of the normalizing constant |

`varest` |
the variance of the estimate of the normalizing constant |

As always with importance sampling the procedure can be very unstable, particularly for large *k*. Hence rerunning the function with different simulation sample sizes, and different `gmu`

and `gsigma`

is recommended

Jon Wakefield ([email protected])

Wakefield, J. (2010). Bayesian methods for examining Hardy-Weinberg equilibrium. Biometrics; Vol 66:257-65

Weir, B.S. (1996). Genetic Data Analysis II. Sunderland MA: Sinauer.

`LambdaOptim`

, `DirichNormSat`

, `DirichNormHWE`

, `TriangNormHWE`

1 2 3 4 5 6 7 8 9 10 11 12 13 | ```
alpha <- c(1,1,1,1) # prior on allele frequencies
# gmu and gsigma were obtained from a WinBUGS run
gmu <- c(-0.4633092,0.3391625,0.3397936,-3.5438008)
gsigma <- matrix(c(
0.07937341,0.02819656,0.02766583,0.04607996,
0.02819656,0.07091320,0.04023827,0.01657028,
0.02766583,0.04023827,0.07042278,0.01752266,
0.04607996,0.01657028,0.01752266,0.57273683),nrow=4,ncol=4)
data(DiabRecess)
HWEImportSamp(nsim=5000,nvec=DiabRecess,ischoice=1,lambdamu=-2.95,
lambdasd=1.07,alpha=alpha,gmu,gsigma)
HWEImportSamp(nsim=5000,nvec=DiabRecess,ischoice=2,lambdamu=-2.95,
lambdasd=1.07,alpha=alpha)
``` |

HWEBayes documentation built on May 30, 2017, 2:34 a.m.

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