limma (version 3.28.6)

TestResults-class: Matrix of Test Results - class

Description

A matrix-based class for storing the results of simultanous tests. TestResults objects are normally created by decideTests, classifyTestsF, classifyTestsT or classifyTestsP.

Usage

## S3 method for class 'TestResults':
summary(object, \dots)

Arguments

object

object of class TestResults

...

other arguments are not used

Slots/List Components

A TestResults object is essentially a numeric matrix with elements equal to 0, 1 or -1. Zero represents acceptance of the null hypothesis, 1 indicates rejection in favor of the right tail alternative and -1 indicates rejection in favor of the left tail alternative. TestResults objects can be created by new("TestResults",results) where results is a matrix. Objects of this class contain no slots (other than .Data), although the attributes dim and dimnames may be treated as slots.

Methods

This class inherits directly from class matrix so any operation appropriate for matrices will work on objects of this class. show and summary methods are also implemented. Functions in LIMMA which operate on TestResults objects include heatDiagram, vennCounts, vennDiagram, write.fit.

See Also

02.Classes gives an overview of all the classes defined by this package. 08.Tests gives an overview of multiple testing.

Examples

#  Assume a data object MA and a design matrix
fit <- lmFit(MA, design)
fit <- eBayes(fit)
results <- decideTests(fit)
summary(results)