Class "ChrMapHyperGResult"

Description

This class represents the results of a Hypergeometric test for over-representation of genes in a selected gene list in the chromosome band annotation. The hyperGTest function returns an instance of ChrMapHyperGResult when given a parameter object of class ChrMapHyperGParams. For details on accessing the results, see HyperGResult-accessors.

Objects from the Class

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

Slots

pvalue.order:

Object of class "integer" that gives the order of the p-values.

conditional:

Object of class "logical" is a flag indicating whether or not this result is from a conditional analysis.

chrGraph:

Object of class "graph". The nodes are the chromosome bands with edges representing the tree structure of the bands. Each node has a "geneIds" attribute that gives the gene IDs annotated at that band.

annotation:

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

geneIds:

Object of class "ANY": the input vector of gene identifiers intersected with the universe of gene identifiers used in the computation. The class of this slot is specified as "ANY" because gene IDs may be integer or character vectors depending on the annotation package.

testName:

A string identifying the testing method used.

pvalueCutoff:

Numeric value used a a p-value cutoff. Used by the show method to count number of significant terms.

testDirection:

Object of class "character" indicating whether the test was for over-representation ("over") or under-representation ("under").

Extends

Class "HyperGResultBase", directly.

Methods

See HyperGResult-accessors.

Author(s)

Seth Falcon

Examples

showClass("ChrMapHyperGResult")
## For details on accessing the results:
##     help("HyperGResult-accessors")

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/ChrMapHyperGResult-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: ChrMapHyperGResult-class
> ### Title: Class "ChrMapHyperGResult"
> ### Aliases: ChrMapHyperGResult-class conditional,ChrMapHyperGResult-method
> ### Keywords: classes
> 
> ### ** Examples
> 
> showClass("ChrMapHyperGResult")
Class "ChrMapHyperGResult" [package "Category"]

Slots:
                                                                            
Name:   pvalue.order   conditional      chrGraph    annotation       geneIds
Class:       integer       logical         graph     character           ANY
                                                
Name:       testName  pvalueCutoff testDirection
Class:     character       numeric     character

Extends: "HyperGResultBase"
> ## For details on accessing the results:
> ##     help("HyperGResult-accessors")
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>