Description Usage Arguments Author(s) Examples

Compute matrix of simulated Z scores

1 2 3 | ```
simulated_z_score(N0, N1, snps, W, gamma.W, freq,
GenoProbList = make_GenoProbList(snps = snps, W = W, freq = freq),
nrep = 1)
``` |

`N0` |
The number of Y=0 |

`N1` |
The number of Y=1 |

`snps` |
The snps at which we wish to compute the expected Z Score |

`W` |
The true causal SNPs (these need not be in "snps") |

`gamma.W` |
The log odds ratios of effect of the true causal SNPs (not including gamma0, the intercept term) |

`freq` |
Haplotype frequencies as a data.frame, with column Probability indicating relative frequency in controls. |

`GenoProbList` |
An list of objects giving the probability of seeing each X,W genotype vector. This can be calculated within the function if no value supplied, or you can pass a pre-calculated version |

`nrep` |
Number of replicates (simulated vectors of Z scores) under this scenario. Default=1 |

Mary Fortune and Chris Wallace

1 2 3 4 | ```
freq=fake_freq(nhaps=100,nsnps=5) # fake haplotype frequency data
Z=simulated_z_score(N0=1000,N1=2000,snps=paste0("s",1:5),
W="s1",gamma.W=log(1.5),freq=freq,nrep=3)
Z # causal variant is SNP 1, with OR 1.5
``` |

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