simulated_vbeta: Compute a simulated var(beta)
In simGWAS: Fast Simulation of Large Case-Control GWAS Summary Statistics

Description Usage Arguments Details Value Author(s) Examples

Simulate var(beta)

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simulated_vbeta(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

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

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

Mary Fortune and Chris Wallace

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