parentChild-class: Classes "parentChild" and "pC"

In topGO: Enrichment Analysis for Gene Ontology

Description

Classes that extend the "classicCount" class by adding support for the parent-child test.

Objects from the Class

Objects can be created by calls of the form new("parentChild", testStatistic, name, groupMembers, parents, sigMembers, joinFun, ...).

Slots

splitIndex:

Object of class "integer" ~~

joinFun:

Object of class "character" ~~

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

allMembers<-

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

allMembers

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

allParents

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

getSigGroups

signature(object = "topGOdata", test.stat = "parentChild"): ...

initialize

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

joinFun

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

numAllMembers

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

numSigAll

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

sigAllMembers

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

sigMembers<-

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

updateGroup

signature(object = "parentChild", name = "missing", members = "character"): ...

Author(s)

Adrian Alexa

See Also

classicCount-class, groupStats-class, getSigGroups-methods

Examples

showClass("parentChild")
showClass("pC")

Example output

Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, basename, cbind, colnames,
    dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which.max, which.min

Loading required package: graph
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: GO.db
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:base’:

    expand.grid


Loading required package: SparseM

Attaching package: ‘SparseM’

The following object is masked from ‘package:base’:

    backsolve


groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.

Attaching package: ‘topGO’

The following object is masked from ‘package:IRanges’:

    members

Class "parentChild" [package "topGO"]

Slots:
                                                                            
Name:     splitIndex       joinFun   significant          name    allMembers
Class:       integer     character       integer     character     character
                                                
Name:        members testStatistic   testStatPar
Class:     character      function          list

Extends: 
Class "classicCount", directly
Class "groupStats", by class "classicCount", distance 2
Class "pC" [package "topGO"]

Slots:
                                                                            
Name:        joinFun   significant          name    allMembers       members
Class:      function       integer     character     character     character
                                  
Name:  testStatistic   testStatPar
Class:      function          list

Extends: 
Class "classicCount", directly
Class "groupStats", by class "classicCount", distance 2

topGO documentation built on Nov. 8, 2020, 6:55 p.m.