finemap.abf: Bayesian finemapping analysis
In chr1swallace/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
chr1swallace/coloc documentation built on April 13, 2024, 1:05 a.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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