A class for containing a list of ExpressionSets

Description

Each element in the list must be a valid ExpressionSet. The featureNames must be identical for each ExpressionSet.

Objects from the Class

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

Slots

.Data:

Object of class "list"

Extends

Class "list", from data part. Class "vector", by class "list", distance 2. Class class.AssayData, by class "list", distance 2.

Methods

.integrativeCorrelationFilter

signature(object = "ExpressionSetList") Experimental function for filtering an arbitrary list of ExpressionSets by integrative correlation. Genes are excluded that do not exceed the fdr threshold in at least 1 of the studies.

"["

signature(x = "ExpressionSetList") Subsets each ExpressionSet element in the list.

coerce

signature(from = "list", to = "ExpressionSetList") Coerces a list of ExpressionSet objects to an object of class ExpressionSetList. The validityMethod for the ExpressionSetList class will return an error if the featureNames for each ExpressionSet are not identical.

dim

signature(x="ExpressionSetList") applies dim to each element of the list.

featureNames

signature(object = "ExpressionSetList") Accessor for the featureNames

geneCenter

signature(object = "ExpressionSetList") See geneCenter

lapply

signature(object="ExpresssionSetList") Coerces instance of ExpressionSetList to a list and does lapply on the list. Returns an object of class ExpressionSetList

nSamples

signature(x = "ExpressionSetList") Numerical vector giving the number of samples in each ExpressionSet

nrow

signature(x = "ExpressionSetList") Numerical: number of features or genes

pData

signature(object = "ExpressionSetList") returns a list of data.frames. The elements of the list correspond to the studies in the ExpressionSetList object.

phenotype

signature(object="ExpressionSetList", varLabel="character") Accessor for the clinical variable. Assumes that the clinical variable has the same name in each study.

standardizeSamples

signature(object = "ExpressionSetList") See standardizeSamples

studyCenter

signature(object = "ExpressionSetList") See studyCenter

zeroNu

signature(object = "ExpressionSetList") See zeroNu.

Author(s)

R. Scharpf

See Also

XdeMcmc-class, XdeParameter-class

Examples

	showClass("ExpressionSetList")
	data(expressionSetList)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(XDE)
Loading required package: Biobase
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

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Welcome to XDE version 2.18.0
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/XDE/ExpressionSetList-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: ExpressionSetList-class
> ### Title: A class for containing a list of ExpressionSets
> ### Aliases: ExpressionSetList-class
> ###   .integrativeCorrelationFilter,ExpressionSetList-method
> ###   [,ExpressionSetList-method coerce,list,ExpressionSetList-method
> ###   dim,ExpressionSetList-method featureNames,ExpressionSetList-method
> ###   geneCenter,ExpressionSetList-method lapply,ExpressionSetList-method
> ###   nSamples nSamples,ExpressionSetList-method
> ###   nrow,ExpressionSetList-method pData,ExpressionSetList-method
> ###   pca,ExpressionSetList-method
> ###   phenotype,ExpressionSetList,character-method
> ###   standardizeSamples,ExpressionSetList-method
> ###   studyCenter,ExpressionSetList-method zeroNu,ExpressionSetList-method
> ### Keywords: classes
> 
> ### ** Examples
> 
> 	showClass("ExpressionSetList")
Class "ExpressionSetList" [package "XDE"]

Slots:
            
Name:  .Data
Class:  list

Extends: 
Class "list", from data part
Class "vector", by class "list", distance 2
Class "AssayData", by class "list", distance 2
Class "vectorORfactor", by class "list", distance 3
> 	data(expressionSetList)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>