Class "ChrMapLinearMResult"

Description

This class represents the results of a linear model-based test for systematic changes in a per-gene statistic by chromosome band annotation. The linearMTest function returns an instance of ChrMapLinearMResult when given a parameter object of class ChrMapLinearMParams. Most slots can be queried using accessors.

Objects from the Class

Objects can be created by calls of the form new("ChrMapLinearMResult", ...), but is more commonly created by callinf linearMTest

Slots

pvalues:

Object of class "numeric", with the p-values for each term.

pvalue.order:

Object of class "integer", the order vector (increasing) for the p-values.

effectSize:

Object of class "numeric", with the effect size for each term.

annotation:

Object of class "character" ~~

geneIds:

Object of class "ANY" ~~

testName:

Object of class "character" ~~

pvalueCutoff:

Object of class "numeric" ~~

minSize:

Object of class "integer" ~~

testDirection:

Object of class "character" ~~

conditional:

Object of class "logical" ~~

graph:

Object of class "graph" ~~

gsc:

Object of class "GeneSetCollection" ~~

Extends

Class "LinearMResult", directly.

Class "LinearMResultBase", by class "LinearMResult", distance 2.

Methods

None

Author(s)

Deepayan Sarkar, Michael Lawrence

See Also

linearMTest, ChrMapLinearMParams, LinearMResult, LinearMResultBase,

Examples

showClass("ChrMapLinearMResult")

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

Slots:
                                                                              
Name:            pvalues      pvalue.order        effectSize        annotation
Class:           numeric           integer           numeric         character
                                                                              
Name:            geneIds          testName      pvalueCutoff           minSize
Class:               ANY         character           numeric           integer
                                                                              
Name:      testDirection       conditional             graph               gsc
Class:         character           logical             graph GeneSetCollection

Extends: 
Class "LinearMResult", directly
Class "LinearMResultBase", by class "LinearMResult", distance 2
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>