Category (version 2.38.0)

LinearMResult-class: Class "LinearMResult"

Description

This class represents the results of a test for systematic change in some gene-level statistic by gene sets. The linearMTest generic function returns an instance of the LinearMResult class.

Objects from the Class

Objects can be created by calls of the form new("LinearMResult", ...), but is more commonly created using a call to linearMTest.

Slots

pvalues:

Object of class "numeric", with the p-values for each term.

pvalue.order:

Object of class "integer", the order vector (increasing) for the p-values.

effectSize:

Object of class "numeric", with the effect size for each term.

annotation:

Object of class "character" ~~

geneIds:

Object of class "ANY" ~~

testName:

Object of class "character" ~~

pvalueCutoff:

Object of class "numeric" ~~

minSize:

Object of class "integer" ~~

testDirection:

Object of class "character" ~~

conditional:

Object of class "logical" ~~

graph:

Object of class "graph" ~~

gsc:

Object of class "GeneSetCollection" ~~

Extends

Class "LinearMResultBase", directly.

Methods

effectSize

signature(r = "LinearMResult"): ...

pvalues

signature(r = "LinearMResult"): ...

summary

signature(r = "LinearMResult"): returns a data.frame with a row for each gene set tested the following columns: ID, Pvalue, Effect size, Size (number of members), Conditional (whether the test used the conditional test), and TestDirection (for up or down).

See Also

linearMTest

Examples

showClass("LinearMResult")