Description Usage Arguments Details Value Author(s) Examples

Estimate the expected variance of beta. This is approximately expected(1/var(U)).

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

`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 |

Assumes we have a list, GenoProbList, giving the GenoProb values for each X.

The expected variance of beta for each SNP X, assuming the causal SNPs are W

Mary Fortune and Chris Wallace

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

simGWAS documentation built on Aug. 22, 2019, 9:03 a.m.

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