wakefield_null_pp: compute reciprocal posterior probabilities using Wakefield's...
In ollyburren/cupcake: PCA for GWAS

compute reciprocal posterior probabilities using Wakefield's approximate Bayes Factors wakefield_null_pp computes posterior probabilities for a given SNP to be NOT be causal for a given SNP under the assumption of a single causal variant.

1	wakefield_null_pp(p, f, N, s, pi_i = 1e-04, sd.prior = 0.2)

`p`	a vector of univariate pvalues from a GWAS
`f`	a vector of minor allele frequencies taken from some reference population.
`N`	a scalar or vector for total sample size of GWAS
`s`	a scalar representing the proportion of cases (n.cases/N)
`pi_i`	a scalar representing the prior probability (DEFAULT 1 \times 10^{-4})
`sd.prior`	a scalar representing our prior expectation of β (DEFAULT 0.2). The method assumes a normal prior on the population log relative risk centred at 0 and the DEFAULT value sets the variance of this distribution to 0.04, equivalent to a 95% belief that the true relative risk is in the range of 0.66-1.5 at any causal variant.