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.

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)

[Package XDE version 2.28.0 Index]