Simulate var(beta)

simulated_vbeta(N0, N1, snps, W, gamma.W, freq,
  GenoProbList = make_GenoProbList(snps = snps, W = W, freq = freq),
  nrep = 1)

Arguments

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

Value

A simulated variance of beta for each SNP X, assuming the causal SNPs are W

Details

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

Examples

freq=fake_freq(nhaps=100,nsnps=5) # fake haplotype frequency data VB=simulated_vbeta(N0=1000,N1=2000,snps=paste0("s",1:5), W="s1",gamma.W=log(1.5),freq=freq) VB # causal variant is SNP 1, with OR 1.5
#> [,1] [,2] [,3] [,4] [,5] #> [1,] 0.003442928 0.003969581 0.003749157 0.003046727 0.002964443