AnnotationAffx: The AnnotationAffx class

In IdMappingRetrieval: ID Mapping Data Retrieval

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:

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

Author(s)

Alex Lisovich, Roger Day

IdMappingRetrieval documentation built on Oct. 31, 2019, 8:08 a.m.