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Description: computing p-values by hand as gominer is not packaged in Debian
Author: Pierre Gruet <pgt@debian.org>
Forwarded: https://github.com/CampagneLaboratory/goby3/issues/4
Last-Update: 2021-08-05
--- a/goby-distribution/pom.xml
+++ b/goby-distribution/pom.xml
@@ -382,5 +382,10 @@
<artifactId>goby-io</artifactId>
<version>${project.version}</version>
</dependency>
+ <dependency>
+ <groupId>distlib</groupId>
+ <artifactId>distlib</artifactId>
+ <version>debian</version>
+ </dependency>
</dependencies>
</project>
--- a/goby-distribution/src/main/java/org/campagnelab/goby/stats/FisherExactTestCalculator.java
+++ b/goby-distribution/src/main/java/org/campagnelab/goby/stats/FisherExactTestCalculator.java
@@ -18,7 +18,7 @@
package org.campagnelab.goby.stats;
-import gominer.Fisher;
+import DistLib.hypergeometric;
import it.unimi.dsi.fastutil.objects.ObjectArraySet;
/**
@@ -97,9 +97,21 @@
* x+y
* @return 2-tailed gominer.Fisher p value
*/
- // public double fisher(final int totalChanged, final int changedInNode, final int total, final int inNode) {
- final Fisher fisher = new Fisher();
- final double pValue = fisher.fisher(totalCountInA, sumCountInA, totalCountInA + totalCountInB, sumCountInA + sumCountInB);
+ //Variables names for the analogy with R arguments.
+ double x = sumCountInA;
+ double whiteBalls = sumCountInA + sumCountInB;
+ double blackBalls = totalCountInA + totalCountInB - whiteBalls;
+ double n = totalCountInA;
+ double sumProba = 0.;
+ //Determining the probability of the given grid under the null hypothesis.
+ double probabilityGrid = hypergeometric.density(x, whiteBalls, blackBalls, n);
+ //Computing the p-value by summing the probabilities of grids that are at least as unlikely as the current one.
+ for (double i = Math.max(0, n - blackBalls) ; i < Math.min(n, whiteBalls) + 1.E-13 ; i++) {
+ double thisProba = hypergeometric.density(i, whiteBalls, blackBalls, n);
+ if (thisProba < probabilityGrid + 1.E-13) {
+ sumProba += thisProba;
+ }
+ }
/* Test : fisher.fisher(40,10,100,30)=
@@ -113,7 +125,7 @@
------------------------------------------
*/
info.statistics.size(results.getNumberOfStatistics());
- info.statistics.set(fisherPValuesStatIndex, pValue);
+ info.statistics.set(fisherPValuesStatIndex, sumProba);
return info;
}
--- a/goby-distribution/src/test/java/org/campagnelab/goby/R/TestFisherExact.java
+++ b/goby-distribution/src/test/java/org/campagnelab/goby/R/TestFisherExact.java
@@ -18,7 +18,7 @@
package org.campagnelab.goby.R;
-import gominer.Fisher;
+import DistLib.hypergeometric;
import org.apache.commons.lang.ArrayUtils;
import org.junit.AfterClass;
import static org.junit.Assert.assertEquals;
@@ -157,11 +157,24 @@
*/
@Test
public void twoTailed() {
- final Fisher gominer = new Fisher();
- final double gominerPValue = gominer.fisher(40, 10, 100, 30);
+ //Variables names for the analogy with R arguments.
+ double x = 10;
+ double whiteBalls = 30;
+ double blackBalls = 70;
+ double n = 40;
+ double sumProba = 0.;
+ //Determining the probability of the given grid under the null hypothesis.
+ double probabilityGrid = hypergeometric.density(x, whiteBalls, blackBalls, n);
+ //Computing the p-value by summing the probabilities of grids that are at least as unlikely as the current one.
+ for (double i = Math.max(0, n - blackBalls) ; i < Math.min(n, whiteBalls) + 1.E-13 ; i++) {
+ double thisProba = hypergeometric.density(i, whiteBalls, blackBalls, n);
+ if (thisProba < probabilityGrid + 1.E-13) {
+ sumProba += thisProba;
+ }
+ }
final double fisherExactPValue = FisherExact.twoTailed(40, 10, 100, 30);
- assertEquals("R result does not match gominer", gominerPValue, fisherExactPValue, EPSILON);
+ assertEquals("R result does not match hand-computed", sumProba, fisherExactPValue, EPSILON);
}
/**
--- a/goby-distribution/src/test/java/org/campagnelab/goby/stats/TestStatistics.java
+++ b/goby-distribution/src/test/java/org/campagnelab/goby/stats/TestStatistics.java
@@ -19,7 +19,7 @@
package org.campagnelab.goby.stats;
import org.campagnelab.goby.R.FisherExact;
-import gominer.Fisher;
+import DistLib.hypergeometric;
import it.unimi.dsi.fastutil.objects.ObjectArrayList;
import it.unimi.dsi.lang.MutableString;
import org.apache.commons.math.MathException;
@@ -371,15 +371,27 @@
assertEquals("fisher test equal expected result", 0.5044757698516504, results.getStatistic(info, fisher.statisticIds.get(0)), 0.001);
- final Fisher fisherTest = new Fisher();
final int totalCountInA = 1700;
final int totalCountInB = 170; // equal total in each group
final int sumCountInA = 90;
final int sumCountInB = 45; // half the counts in sample B
+ //Variables names for the analogy with R arguments.
+ double x = sumCountInA;
+ double whiteBalls = sumCountInA + sumCountInB;
+ double blackBalls = totalCountInA + totalCountInB - whiteBalls;
+ double n = totalCountInA;
+ double sumProba = 0.;
+ //Determining the probability of the given grid under the null hypothesis.
+ double probabilityGrid = hypergeometric.density(x, whiteBalls, blackBalls, n);
+ //Computing the p-value by summing the probabilities of grids that are at least as unlikely as the current one.
+ for (double i = Math.max(0, n - blackBalls) ; i < Math.min(n, whiteBalls) + 1.E-13 ; i++) {
+ double thisProba = hypergeometric.density(i, whiteBalls, blackBalls, n);
+ if (thisProba < probabilityGrid + 1.E-13) {
+ sumProba += thisProba;
+ }
+ }
- fisherTest.fisher(totalCountInA, sumCountInA, totalCountInA + totalCountInB, sumCountInA + sumCountInB);
-
- final double pValue = fisherTest.getTwotail();
+ final double pValue = sumProba;
final double proportionTotalA = divide(totalCountInA, (totalCountInA + totalCountInB));
final double proportionTotalB = divide(totalCountInB, (totalCountInA + totalCountInB));
final ChiSquareTest chisquare = new ChiSquareTestImpl();
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