Selection {Bayenet} | R Documentation |
Variable selection for a Bayenet object
Description
Variable selection for a Bayenet object
Usage
Selection(obj, sparse)
Arguments
obj |
Bayenet object. |
sparse |
logical flag. If TRUE, spike-and-slab priors will be used to shrink coefficients of irrelevant covariates to zero exactly. |
Details
For class ‘Sparse’, the inclusion probability is used to indicate the importance of predictors.
Here we use a binary indicator \phi
to denote the membership of the non-spike distribution.
Take the main effect of the j
th genetic factor, X_{j}
, as an example.
Suppose we have collected H posterior samples from MCMC after burn-ins. The j
th G factor is included
in the final model at the j
th MCMC iteration if the corresponding indicator is 1, i.e., \phi_j^{(h)} = 1
.
Subsequently, the posterior probability of retaining the j
th genetic main effect in the final model is defined as the average of all the indicators for the j
th G factor among the H posterior samples.
That is, p_j = \hat{\pi} (\phi_j = 1|y) = \frac{1}{H} \sum_{h=1}^{H} \phi_j^{(h)}, \; j = 1, \dots,p.
A larger posterior inclusion probability of j
th indicates a stronger empirical evidence that the j
th genetic main effect has a non-zero coefficient, i.e., a stronger association with the phenotypic trait.
Here, we use 0.5 as a cutting-off point. If p_j > 0.5
, then the j
th genetic main effect is included in the final model. Otherwise, the j
th genetic main effect is excluded in the final model.
For class ‘NonSparse’, variable selection is based on 95% credible interval.
Please check the references for more details about the variable selection.
Value
an object of class ‘Selection’ is returned, which is a list with components:
method |
method used for identifying important effects. |
effects |
a list of indicators of selected effects. |
References
Lu, X. and Wu, C. (2023). Bayesian quantile elastic net with spike-and-slab priors.
See Also
Examples
data(dat)
max.steps=5000
fit= Bayenet(X, Y, clin, max.steps, penalty="lasso")
selected=Selection(fit,sparse=TRUE)
selected$Main.G