AssayData-class           package: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'

