Class "elimExpr"

Description

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

Details

TODO: Some datails here.....

Objects from the Class

Objects can be created by calls of the form new("elimExpr", testStatistic, name, groupMembers, exprDat, pType, elim, cutOff, ...). ~~ describe objects here ~~

Slots

cutOff:

Object of class "numeric" ~~

elim:

Object of class "integer" ~~

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 "weight01Expr", directly. Class "classicExpr", by class "weight01Expr", distance 2. Class "groupStats", by class "weight01Expr", distance 3.

Methods

cutOff<-

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

cutOff

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

getSigGroups

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

initialize

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

Author(s)

Adrian Alexa

See Also

classicScore-class, groupStats-class, getSigGroups-methods

Examples

showClass("elimExpr")

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(topGO)
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, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, 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, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

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 objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums


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

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/topGO/elimExpr-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: elimExpr-class
> ### Title: Class "elimExpr"
> ### Aliases: leaExpr-class elimExpr-class weight01Expr-class
> ###   depth,leaExpr-method depth<-,leaExpr-method cutOff<-,elimExpr-method
> ###   cutOff,elimExpr-method initialize,leaExpr-method
> ###   initialize,elimExpr-method initialize,weight01Expr-method
> ###   allMembers,weight01Expr-method elim<-,weight01Expr-method
> ###   elim,weight01Expr-method members,weight01Expr,missing-method
> ###   numAllMembers,weight01Expr-method numMembers,weight01Expr-method
> ### Keywords: classes
> 
> ### ** Examples
> 
> showClass("elimExpr")
Class "elimExpr" [package "topGO"]

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

Extends: 
Class "weight01Expr", directly
Class "classicExpr", by class "weight01Expr", distance 2
Class "groupStats", by class "weight01Expr", distance 3
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>