AnnotationAffx: The AnnotationAffx class

Description

Package: Class AnnotationAffx Object ~~| ~~+--Annotation ~~~~~~~| ~~~~~~~+--AnnotationAffx Directly known subclasses: AnnotationNetAffx public static class AnnotationAffx extends Annotation The AnnotationAffx class encapsulates the functionality allowing to retrieve data from the Affymetrix annotation data online repository through the getIdMap() and getDataFrame() calls.

Usage

AnnotationAffx(cacheFolderName="Affymetrix", primaryColumn="Probe.Set.ID", secondaryColumn="SwissProt", swap=TRUE, ...)

Arguments

cacheFolderName

The path to a service cashing directory for a given AnnotationAffx object. The path is relative to the caching subsystem root directory. Default is 'Affymetrix'

primaryColumn

Primary column to be retrieved from a data frame obtained from the Affymetrix annotation repository when getIdMap() is called. Default is 'Probe.Set.ID'.

secondaryColumn

Secondary column to be retrieved from a data frame obtained from the Affymetrix annotation repository when getIdMap() is called. Default is 'SwissProt'.

swap

Logical indicating if primary and secondary column(s) need to be swapped at the end of the IdMap retrieval during the getIdMap() call.Default is TRUE.

...

Additional parameters, see Annotation.

Fields and Methods

Methods: rll{ }

Methods inherited from Annotation: getArrayType, getArrayTypes, getColumns, getCredentials, getDataFrame, getFolderName, getIdMap, getRoot, getServiceRoot, init, readDF, setCredentials, setOptions

Methods inherited from Object: $, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clone, detach, equals, extend, finalize, gc, getEnvironment, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, objectSize, print, registerFinalizer, save