zzz-ARRCompatibility-class {AffyCompatible} | R Documentation |
These classes and methods facilitate navigation of the Affymetrix ARR sample attribute files. ARR files are generated by the Affymetrix AGCC (GeneChiptextregistered{} Command Console) application. Specifically, the classes are R representations of the Affymetrix classes defined in ArraySetAndTemplateFile.dtd. The 'show' methods for these classs indicate how objects are to be accessed; details are in the `Retrieving MAGE and ARR sample attributes' vignette.
Objects are created internally, by parsing XML retrieved from ARR, and are not created directly by the user.
Objects have a variety of slots. To discover slot names and content
type, see the slotNames
portion of the example, below.
Class "ARRCompatibility"
, directly.
Class "AffyCompatible"
, by class "ARRCompatibility", distance 2.
'Accessor' methods are defined on auto-generated classes to access slot content.
Accessors are apparent from displaying the object; each line of the
display is of the form accessor: content
. To retrieve the
content of an instance object
, invoke accessor(object)
.
Some objects contains several instances of another object. These
'typed associations' are represented by the
.TypedAssociation
class, and are navigated or
subset as one would a standard R vector, e.g., using [
,
[[
. A useful paradigm for displaying all instances is
illustrated in the vignette.
Martin Morgan <mtmorgan@fhcrc.org>
Vignette `Retrieving MAGE and ARR sample attributes'.
## defined and auto-generated classes names(slot(getClass("ARRCompatibility", where=getNamespace("AffyCompatible")), "subclasses"))