EBEN (version 4.1)

EBelasticNet.GaussianCV: Cross Validation (CV) Function to Determine Hyperparameters of the EBEN Algorithm for Gaussian Model

Description

Hyperparameter controls degree of shrinkage, and is obtained via Cross Validation (CV). This program calculates the maximum lambda that allows one non-zero basis; and performs a search down to 0.0001*lambda_max at even steps. (20 steps)

Usage

EBelasticNet.GaussianCV(BASIS, Target, nFolds, Epis = "no",foldId)

Arguments

BASIS

sample matrix; rows correspond to samples, columns correspond to features

Target

Response each individual

nFolds

number of n-fold cv

Epis

"yes" or "no" for including two-way interactions

foldId

random assign samples to different folds

Value

• CrossValidation
  col1: hyperparameter; col2: loglikelihood mean; standard ERROR of nfold mean log likelihood
• Lmabda_optimal
  the optimal hyperparameter as computed
• Alpha_optimal
  the optimal hyperparameter as computed

Details

If Epis="yes", the program adds two-way interaction K*(K-1)/2 more columns to BASIS

References

Huang, A., Xu, S., and Cai, X. (2013). Empirical Bayesian elastic net for multiple quantitative trait locus mapping. submitted.

Examples

library(EBEN)
data(BASIS)
data(y)
#reduce sample size to speed up the running time
n = 50;
k = 100;
BASIS = BASIS[1:n,1:k];
y  = y[1:n];
CV = EBelasticNet.GaussianCV(BASIS, y, nFolds = 3,Epis = "no")