+
+Package uk.ac.ebi.utils.statistics
+Class FisherExact
+java.lang.Object
+
+uk.ac.ebi.utils.statistics.FisherExact
++ +
Class for Fisher Exact test.
+
+
+This was copied and adapted from + here, + (commit 71b68de, 2023/07/17), since the original class is part of a bigger project concerning a different + specific application domain.
+ +TODO: It would be better to have a cached object that depends on maxSize as cache key, ie,
+ when a requested maxSize is < cached maxSize, the existing instance is returned,
+ else a new instance is created that replaces the old one. This also requires that such
+ instance has an expiration time, a cache that evicts automatically and an ability to initialise
+ a FisherExact with a bigger size from one with a smaller one. At that point, we
+ would prefer static wrapper methods for methods like getP(int, int, int, int).
Original comments
+ + This does a Fisher Exact test. The Fisher's Exact test procedure calculates an exact probability value for the + relationship between two dichotomous variables, as found in a two by two crosstable. The program calculates the + difference between the data observed and the data expected, considering the given marginal and the assumptions of + the model of independence. It works in exactly the same way as the Chi-square test for independence; however, the + Chi-square gives only an estimate of the true probability value, an estimate which might not be very accurate if + the marginal is very uneven or if there is a small value (less than five) in one of the cells. + + It uses an array of factorials initialized at the beginning to provide speed. There could be better ways to do + this.-
+
- Version: +
- $Id: FisherExact.java,v 1 +
- Author: +
- Ed Buckler +
-
+
+
-
+
+ +Constructor Summary
+Constructors+ +
+
+ -
+
+ +Method Summary
++ ++ +++++Modifier and Type+Method+Description++final double+getCumlativeP(int a, + int b, + int c, + int d) ++Calculates the one-tail P-value for the Fisher Exact test.++final double+getLeftTailedP(int a, + int b, + int c, + int d) ++Calculates the left-tail P-value for the Fisher Exact test.++static double+getOddsRatio(double a, + double b, + double c, + double d) ++Measure of how far from independence the 2x2 table is.++static double[]+getOddsRatioAnd95thConfidenceInterval(double a, + double b, + double c, + double d) ++Returns OR, lower, upper++final double+getP(int a, + int b, + int c, + int d) ++calculates the P-value for this specific state++final double+getRightTailedP(int a, + int b, + int c, + int d) ++Calculates the right-tail P-value for the Fisher Exact test.++final double+getTwoTailedP(int a, + int b, + int c, + int d) ++Calculates the two-tailed P-value for the Fisher Exact test.+
+
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+
+
-
+
+ +Constructor Details
+-
+
-
+
+ +FisherExact
+public FisherExact+(int maxSize) constructor for FisherExact table+-
+
- Parameters: +
maxSize- is the maximum sum that will be encountered by the table (a+b+c+d)
+
+
+
+ -
+
-
+
+ +Method Details
+-
+
-
+
+ +getP
+public final double getP+(int a, + int b, + int c, + int d) calculates the P-value for this specific state+-
+
- Parameters: +
a- a, b, c, d are the four cells in a 2x2 matrix
+b-
+c-
+d-
+- Returns: +
- the P-value +
+ -
+
+ +getCumlativeP
+public final double getCumlativeP+(int a, + int b, + int c, + int d) Calculates the one-tail P-value for the Fisher Exact test. Determines whether to calculate the right- or left- + tail, thereby always returning the smallest p-value. + + a, b, c, d are the four cells in a 2x2 matrix+-
+
- Returns: +
- one-tailed P-value (right or left, whichever is smallest) +
+ -
+
+ +getRightTailedP
+public final double getRightTailedP+(int a, + int b, + int c, + int d) Calculates the right-tail P-value for the Fisher Exact test. + + a, b, c, d are the four cells in a 2x2 matrix+-
+
- Returns: +
- one-tailed P-value (right-tail) +
+ -
+
+ +getLeftTailedP
+public final double getLeftTailedP+(int a, + int b, + int c, + int d) Calculates the left-tail P-value for the Fisher Exact test. + + a, b, c, d are the four cells in a 2x2 matrix+-
+
- Returns: +
- one-tailed P-value (left-tail) +
+ -
+
+ +getTwoTailedP
+public final double getTwoTailedP+(int a, + int b, + int c, + int d) Calculates the two-tailed P-value for the Fisher Exact test. + + In order for a table under consideration to have its p-value included in the final result, it must have a p-value + less than the original table's P-value, i.e. Fisher's exact test computes the probability, given the observed + marginal frequencies, of obtaining exactly the frequencies observed and any configuration more extreme. By "more + extreme," we mean any configuration (given observed marginals) with a smaller probability of occurrence in the + same direction (one-tailed) or in both directions (two-tailed). + + a, b, c, d are the four cells in a 2x2 matrix+-
+
- Returns: +
- two-tailed P-value or NaN if the table sum exceeds the maxSize +
+ -
+
+ +getOddsRatioAnd95thConfidenceInterval
+public static double[] getOddsRatioAnd95thConfidenceInterval+(double a, + double b, + double c, + double d) Returns OR, lower, upper+
+ -
+
+ +getOddsRatio
+public static double getOddsRatio+(double a, + double b, + double c, + double d) Measure of how far from independence the 2x2 table is. 1= independent. Ratio of ratios. Will return Infinity or 0 + if cells are zero.+
+
+ -
+