R: Class "AssayData"

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

combine
  `signature(x = "AssayData", y = "AssayData")`: This method uses `cbind` to create new AssayData elements that contain the samples of both arguments `x` and `y`.

  Both AssayData arguments to combine must have the same collection of elements. The elements must have identical numbers of rows (features). The numerical contents of any columns (samples) present in the same element of different AssayData must be identical. The storageMode of the AssayData arguments must be identical, and the function returns an AssayData with storageMode matching the incoming mode. See also `combine,eSet,eSet-method`

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:

assayData[[name]]
  Select element `name` from `assayData`.
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, matrices are of the same dimension, and `featureNames` (rownames) are consistent (identical or `NULL`) across entries.
assayDataElement(object, element)
  See `eSet-class`
assayDataElementReplace(object, element, value)
  See `eSet-class`
assayDataElementNames(object)
  See `eSet-class`

### Author(s)

Biocore

### See Also

`eSet-class` `ExpressionSet-class`

[Package Biobase version 2.8.0 Index]