gedi.lfc.foldchange.PosteriorMeanLog2FoldChange.java Source code

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Here is the source code for gedi.lfc.foldchange.PosteriorMeanLog2FoldChange.java

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/**
 * 
 *    Copyright 2017 Florian Erhard
 *
 *   Licensed under the Apache License, Version 2.0 (the "License");
 *   you may not use this file except in compliance with the License.
 *   You may obtain a copy of the License at
 *
 *       http://www.apache.org/licenses/LICENSE-2.0
 *
 *   Unless required by applicable law or agreed to in writing, software
 *   distributed under the License is distributed on an "AS IS" BASIS,
 *   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 *   See the License for the specific language governing permissions and
 *   limitations under the License.
 * 
 */
package gedi.lfc.foldchange;

import gedi.lfc.Log2FoldChange;

import org.apache.commons.math3.special.Gamma;

public class PosteriorMeanLog2FoldChange implements Log2FoldChange {

    private double priorA = 1;
    private double priorB = 1;

    /**
     * These are the prior parameters, i.e. for no pseudocounts, use 1!
     * @param priorA
     * @param priorB
     */
    public PosteriorMeanLog2FoldChange(double priorA, double priorB) {
        this.priorA = priorA;
        this.priorB = priorB;
    }

    @Override
    public double computeFoldChange(double a, double b) {
        if (Double.isNaN(a) || Double.isNaN(b))
            return Double.NaN;
        return (Gamma.digamma(a + priorA) - Gamma.digamma(b + priorB)) / Math.log(2);
    }

}