Compute vector of expected Z Scores

Source: R/zscore.R

Compute vector of expected Z scores

expected_z_score(N0, N1, snps, W, gamma.W, freq,
  GenoProbList = make_GenoProbList(snps = snps, W = W, freq = freq))

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

Value

The expected Z Score for all snps in snps, assuming the causal SNPs are W

Examples

freq=fake_freq(nhaps=100,nsnps=5) # fake haplotype frequency data
EZ=expected_z_score(N0=1000,N1=2000,snps=paste0("s",1:5),
                    W="s1",gamma.W=log(1.5),freq=freq)
EZ # causal variant is SNP 1, with OR 1.5
#> [1] 6.727084 4.170406 3.385346 3.158742 2.250039