Class "ChrMapLinearMParams"

Description

This class encapsulates parameters needed for testing systematic variations in some gene-level statistic by chromosome bands using linearMTest.

Objects from the Class

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

Slots

graph:

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.

gsc:

The GeneSetCollection object grouping the gene ids into sets.

geneStats:

Named vector of class "numeric", giving the gene-level statistics to be used in the tests.

universeGeneIds:

Object of class "ANY": A vector of gene ids 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.

datPkg:

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

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.

minSize:

An integer giving a minimum size for a gene set for it to be tested. The default is 5.

testDirection:

A string indicating whether the test should test for systematic increase ("up") or decrease ("down") in the geneStats values within a gene set relative to the remaining genes.

Extends

Class "LinearMParams", directly.

Author(s)

Deepayan Sarkar

See Also

linearMTest

Examples

showClass("ChrMapLinearMParams")

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

Slots:
                                                                              
Name:          geneStats   universeGeneIds        annotation            datPkg
Class:           numeric               ANY         character            DatPkg
                                                                              
Name:  categorySubsetIds      categoryName      pvalueCutoff           minSize
Class:               ANY         character           numeric           integer
                                                                              
Name:      testDirection             graph       conditional               gsc
Class:         character             graph           logical GeneSetCollection

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