elimScore-class: Classes "elimScore" and "weight01Score"

In topGO: Enrichment Analysis for Gene Ontology

Description

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

Details

TODO:

Objects from the Class

Objects can be created by calls of the form new("elimScore", testStatistic, name, allMembers, groupMembers, score, alternative, elim, cutOff, ...). ~~ describe objects here ~~

Slots

elim:

Object of class "integer" ~~

cutOff:

Object of class "numeric" ~~

score:

Object of class "numeric" ~~

.alternative:

Object of class "logical" ~~

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

Methods

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

Author(s)

Adrian Alexa

See Also

classicScore-class, groupStats-class, getSigGroups-methods

Examples

##---- Should be DIRECTLY executable !! ----

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

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