elimCount-class: Classes "elimCount" and "weight01Count"

In hxin/topOnto: ontology enrichment analysis

Description

Classes that extend the "classicCount" class by adding a slot representing the members that need to be removed.

Objects from the Class

Objects can be created by calls of the form new("elimCount", testStatistic, name, allMembers, groupMembers, sigMembers, elim, cutOff, ...).

Slots

elim:

Object of class "integer" ~~

cutOff:

Object of class "numeric" ~~

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" ~~

testStatPar:

Object of class "list" ~~

Extends

Class "classicCount", directly. Class "groupStats", by class "classicCount", distance 2.

Methods

No methods defined with class "elimCount" in the signature.

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]]
elim.genes <- sample(go.genes, length(go.genes) / 4)
sig.genes <- sigGenes(GOdata)
elim.group <- new("elimCount", testStatistic = GOFisherTest, name = "fisher",allMembers = gene.universe, groupMembers = go.genes,sigMembers = sig.genes, elim = elim.genes)
contTable(elim.group)
runTest(elim.group)

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