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]