ExpressionSetList-class {XDE}R Documentation

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.
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.
.pca
signature(object = "ExpressionSetList") Runs principal components to generate cross-study summary scores of differential expression in multiple studies. Not meant to be called directly. See xsScores.
standardizeSamples
signature(object = "ExpressionSetList") See standardizeSamples
studyCenter
signature(object = "ExpressionSetList") See studyCenter
xapply
signature(object="ExpressionSetList") An lapply for ExpressionSetList instances. See xapply.
zeroNu
signature(object = "ExpressionSetList") See `zeroNu.

Author(s)

R. Scharpf

See Also

XdeMcmc-class, XdeParameter-class

Examples

showClass("ExpressionSetList")
data(expressionSetList)

[Package XDE version 1.2.0 Index]