Class "ChrMapHyperGParams"

Description

This class encapsulates parameters needed for Hypergeometric testing of over or under representation of chromosome bands among a selected gene list using hyperGTest.

Objects from the Class

Objects can be created by calls of the form new("ChrMapHyperGParams", ...).

Slots

chrGraph:

Object of class "graph". The nodes are the chromosome bands and the edges describe the tree structure of the bands. Each node has a "geneIds" node attributes (see nodeData) which contains a vector of gene IDs annotated at the given band.

conditional:

Object of class "logical", indicating whether the test performed should be a conditional test.

geneIds:

Object of class "ANY": A vector of gene identifiers. Numeric and character vectors are probably the only things that make sense. These are the gene ids for the selected gene set.

universeGeneIds:

Object of class "ANY": A vector of gene ids in the same format as geneIds defining a subset of the gene ids on the chip that will be used as the universe for the hypergeometric calculation. If this is NULL or has length zero, then all gene ids on the chip will be used.

annotation:

A string giving the name of the annotation data package for the chip used to generate the data.

categorySubsetIds:

Object of class "ANY": If the test method supports it, can be used to specify a subset of category ids to include in the test instead of all possible category ids.

categoryName:

A string describing the category. Usually set automatically by subclasses. For example "GO".

pvalueCutoff:

The p-value to use as a cutoff for significance for testing methods that require it. This value will also be passed on to the result instance and used for display and counting of significant results. The default is 0.01.

testDirection:

A string indicating whether the test should be for overrepresentation ("over") or underrepresentation ("under").

datPkg:

Object of class "DatPkg" used to assist with dispatch based on type of annotation data available.

Extends

Class "HyperGParams", directly.

Methods

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

Author(s)

Seth Falcon

Examples

showClass("ChrMapHyperGParams")

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(Category)
Loading required package: stats4
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: AnnotationDbi
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: 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: Matrix

Attaching package: 'Matrix'

The following object is masked from 'package:S4Vectors':

    expand

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/Category/ChrMapHyperGParams-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: ChrMapHyperGParams-class
> ### Title: Class "ChrMapHyperGParams"
> ### Aliases: ChrMapHyperGParams-class conditional,ChrMapHyperGParams-method
> ###   conditional<-,ChrMapHyperGParams,logical-method
> ### Keywords: classes
> 
> ### ** Examples
> 
> showClass("ChrMapHyperGParams")
Class "ChrMapHyperGParams" [package "Category"]

Slots:
                                                                              
Name:           chrGraph       conditional           geneIds   universeGeneIds
Class:             graph           logical               ANY               ANY
                                                                              
Name:         annotation            datPkg categorySubsetIds      categoryName
Class:         character            DatPkg               ANY         character
                                          
Name:       pvalueCutoff     testDirection
Class:           numeric         character

Extends: "HyperGParams"
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>