classicCount-class: Class "classicCount"

In hxin/topOnto: ontology enrichment analysis

Description

This class that extends the virtual class "groupStats" by adding a slot representing the significant members.

Details

This class is used for test statistic based on counts, like Fisher's exact test

Objects from the Class

Objects can be created by calls of the form new("classicCount", testStatistic = "function", name = "character", allMembers = "character", groupMembers = "character", sigMembers = "character").

Slots

significant

Object of class "integer"

name

Object of class "character"

allMembers

Object of class "character"

members

Object of class "character"

testStatistic

Object of class "function"

Extends

Class "groupStats", directly.

Methods

contTable

signature(object = "classicCount"): ...

initialize

signature(.Object = "classicCount"): ...

numSigAll

signature(object = "classicCount"): ...

numSigMembers

signature(object = "classicCount"): ...

sigAllMembers

signature(object = "classicCount"): ...

sigMembers<-

signature(object = "classicCount"): ...

sigMembers

signature(object = "classicCount"): ...

Author(s)

Adrian Alexa

See Also

classicScore-class, groupStats-class, getSigGroups-methods

Examples

data(ONTdata)
gene.universe <- genes(GOdata)
go.genes <- genesInTerm(GOdata, 'DOID:0050709')[[1]]
sig.genes <- sigGenes(GOdata)
my.group <- new("classicCount", testStatistic = GOFisherTest, name = "fisher",allMembers = gene.universe, groupMembers = go.genes,sigMembers = sig.genes)
contTable(my.group)
runTest(my.group)

hxin/topOnto documentation built on May 17, 2019, 9:15 p.m.