Class "classicScore"

Description

A class that extends the virtual class "groupStats" by adding a slot representing the score of each gene. It is used for tests like Kolmogorov-Smirnov test.

Objects from the Class

Objects can be created by calls of the form new("classicScore", testStatistic, name, allMembers, groupMembers, score, decreasing).

Slots

score:

Object of class "numeric" ~~

name:

Object of class "character" ~~

allMembers:

Object of class "character" ~~

members:

Object of class "character" ~~

testStatistic:

Object of class "function" ~~

scoreOrder:

Object of class "character" ~~

testStatPar:

Object of class "ANY" ~~

Extends

Class "groupStats", directly.

Methods

allScore

Method to obtain the score of all members.

scoreOrder

Returns TRUE if the score should be ordered increasing, FALSE otherwise.

membersScore

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

rankMembers

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

score<-

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

Author(s)

Adrian Alexa

See Also

classicCount-class, groupStats-class, getSigGroups-methods

Examples

## define the type of test you want to use
test.stat <- new("classicScore", testStatistic = GOKSTest, name = "KS tests")

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)

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> 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/classicScore-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: classicScore-class
> ### Title: Class "classicScore"
> ### Aliases: classicScore-class scoreOrder membersScore rankMembers score<-
> ###   allScore allScore,classicScore,missing-method
> ###   allScore,classicScore,logical-method scoreOrder,classicScore-method
> ###   initialize,classicScore-method membersScore,classicScore-method
> ###   rankMembers,classicScore-method score<-,classicScore-method
> ###   GOKSTest,classicScore-method GOtTest,classicScore-method
> ###   GOSumTest,classicScore-method GOKSTiesTest,classicScore-method
> ### Keywords: classes
> 
> ### ** Examples
> 
> ## define the type of test you want to use
> test.stat <- new("classicScore", testStatistic = GOKSTest, name = "KS tests")
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>