finemap.abf: Bayesian finemapping analysis
In coloc: Colocalisation Tests of Two Genetic Traits
finemap.abf R Documentation
Bayesian finemapping analysis
Description
Bayesian finemapping analysis
Usage
finemap.abf(dataset, p1 = 1e-04)
Arguments
dataset
a list with specifically named elements defining the dataset
to be analysed. See check_dataset for details.
p1
prior probability a SNP is associated with the trait 1, default 1e-4
Details
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.
Value
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
Author(s)
Chris Wallace
coloc documentation built on Oct. 3, 2023, 5:07 p.m.
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| finemap.abf | R Documentation |
Bayesian finemapping analysis
Description
Bayesian finemapping analysis
Usage
finemap.abf(dataset, p1 = 1e-04)
Arguments
dataset |
a list with specifically named elements defining the dataset
to be analysed. See |
p1 |
prior probability a SNP is associated with the trait 1, default 1e-4 |
Details
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.
Value
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
Author(s)
Chris Wallace
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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