AssayData-class
Class "AssayData"
Container class defined as a class union of list
and
environment
. Designed to contain one or more matrices of the
same dimension.
- Keywords
- classes
Methods
- combine
signature(x = "AssayData", y = "AssayData")
: This method usescbind
to create new AssayData elements that contain the samples of both argumentsx
andy
. 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 alsocombine,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 ofphenoData
.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.
AssayData
include:
- assayData[[name]]
- Select element
name
fromassayData
. - 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 elementsrequired
are present, matrices are of the same dimension, andfeatureNames
(rownames) are consistent (identical orNULL
) across entries. - assayDataElement(object, element)
- See
eSet-class
- assayDataElementReplace(object, element, value)
- See
eSet-class
- assayDataElementNames(object)
- See
eSet-class
See Also
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