wakefield_pp computes posterior probabilities for a given SNP to be causal for a given SNP under the assumption of a single causal variant.wakefield_pp.Rdcompute posterior probabilities using Wakefield's approximate Bayes Factors
wakefield_pp computes posterior probabilities for a given SNP to be causal for a given SNP under the assumption of a single causal variant.
wakefield_pp(p, f, N, s, pi_i = 1e-04, sd.prior = 0.2)
| p | a vector of univariate pvalues from a GWAS |
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| 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 \(\beta\) (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. |
a vector of posterior probabilities.