Bayesian finemapping analysis
Bayesian finemapping analysis
finemap.abf(dataset, p1 = 1e-04)
dataset |
a list with the following elements
Some of these items may be missing, but you must give
|
p1 |
prior probability a SNP is associated with the trait 1, default 1e-4 |
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.
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
Chris Wallace
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