AssayData-class {Biobase}R Documentation

Class "AssayData"

Description

Container class defined as a class union of list and environment. Designed to contain one or more matrices of the same dimension.

Methods

assayData<-
signature(object = "eSet", value = "AssayData"): Replace the AssayData slot of a eSet instance.
combine
signature(x = "AssayData", y = "AssayData"): Return a new AssayData instance with corresponding elements combined using cbind.
featureNames
signature(object = "AssayData")
featureNames<-
signature(object = "AssayData", value = "ANY"): Return or set the feature names as a character vector. These are the row names of the AssayData elements. value can be a character or numeric vector; all entries must be unique.
sampleNames
signature(object = "AssayData")
sampleNames<-
signature(object = "AssayData", value="ANY"): Return or set the sample names. These are the column names of the the AssayData elements and the row names of phenoData. value can be a character or numeric vector.
storageMode
signature(object = "AssayData")
storageMode<-
signature(object = "AssayData", value="character"): Return or set the storage mode for the instance. value can be one of three choices: "lockedEnvironment", "environment", and "list". Environments offer a mechanism for storing data that avoids some of the copying that occurs when using lists. Locked environment help to ensure data integrity. Note that environments are one of the few R objects that are pass-by-reference. This means that if you modify a copy of an environment, you also modify the original. For this reason, we recommend using lockedEnvironment whenever possible.

Additional functions operating on AssayData include:

assayDataNew(storage.mode = c("lockedEnvironment", "environment", "list"), ...)
Use storage.mode to create a new list or environment containing the named elements in ...
assayDataValidMembers(assayData, required)
Validate assayData, ensuring that the named elements required are present and matrices of the same dimension
assayDataElement(object, element)
Return matrix element from assayData object.
assayDataElementReplace(object, element, value)
Set element element in assayData object to matrix value
assayDataElementNames(object)
Return element names in assayData object

Author(s)

Biocore

See Also

eSet-class ExpressionSet-class


[Package Biobase version 1.10.1 Index]