classicExpr-class: Class "classicExpr"

In topGO: Enrichment Analysis for Gene Ontology

Description

This class that extends the virtual class "groupStats" by adding two slots for accomodating gene expression data.

Objects from the Class

Objects can be created by calls of the form new("classicExpr", testStatistic, name, groupMembers, exprDat, pType, ...).

Slots

eData:

Object of class "environment" ~~

pType:

Object of class "factor" ~~

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 "groupStats", directly.

Methods

allMembers<-

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

emptyExpr

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

getSigGroups

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

GOglobalTest

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

initialize

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

membersExpr

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

pType<-

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

pType

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

Author(s)

Adrian Alexa

See Also

classicScore-class, groupStats-class, getSigGroups-methods

Examples

showClass("classicExpr")

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':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, 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 "classicExpr" [package "topGO"]

Slots:
                                                                            
Name:          eData         pType          name    allMembers       members
Class:   environment        factor     character     character     character
                                  
Name:  testStatistic   testStatPar
Class:      function          list

Extends: "groupStats"

Known Subclasses: 
Class "weight01Expr", directly
Class "elimExpr", by class "weight01Expr", distance 2
Class "leaExpr", by class "weight01Expr", distance 2

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