AnnotationAffx {IdMappingRetrieval} | R Documentation |
Package:
Class AnnotationAffx
Object
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Annotation
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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.
AnnotationAffx(cacheFolderName="Affymetrix", primaryColumn="Probe.Set.ID", secondaryColumn="SwissProt", swap=TRUE, ...)
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 |
... |
Additional parameters, see |
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
Alex Lisovich, Roger Day