zzz-ARRCompatibility-class: (Auto-generated) classes and methods for navigating ARR...

Description Objects from the Class Slots Extends Methods Author(s) See Also Examples

Description

These classes and methods facilitate navigation of the Affymetrix ARR sample attribute files. ARR files are generated by the Affymetrix AGCC (GeneChip(R) 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 from the Class

Objects are created internally, by parsing XML retrieved from ARR, and are not created directly by the user.

Slots

Objects have a variety of slots. To discover slot names and content type, see the slotNames portion of the example, below.

Extends

Class "ARRCompatibility", directly. Class "AffyCompatible", by class "ARRCompatibility", distance 2.

Methods

'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.

Author(s)

Martin Morgan <[email protected]>

See Also

Vignette ‘Retrieving MAGE and ARR sample attributes’.

Examples

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## defined and auto-generated classes
names(slot(getClass("ARRCompatibility",
                    where=getNamespace("AffyCompatible")),
           "subclasses"))

AffyCompatible documentation built on May 2, 2018, 2:59 a.m.