Bayesian finemapping analysis
finemap.abf(dataset, p1 = 1e-04)a data.frame:
an annotated version of the input data containing log Approximate Bayes Factors and intermediate calculations, and the posterior probability of the SNP being causal
a list with specifically named elements defining the dataset
to be analysed. See check_dataset for details.
prior probability a SNP is associated with the trait 1, default 1e-4
Chris Wallace
This function calculates posterior probabilities of different causal variant for a single trait.
If regression coefficients and variances are available, it calculates Bayes factors for association at each SNP. If only p values are available, it uses an approximation that depends on the SNP's MAF and ignores any uncertainty in imputation. Regression coefficients should be used if available.