Annotation: The Annotation class

Description Usage Arguments Fields and Methods Author(s)


Class Annotation


Directly known subclasses:
AnnotationAffx, AnnotationEnsembl, AnnotationEnsemblCsv, AnnotationEnvision, AnnotationNetAffx

public abstract static class Annotation
extends Object

This is the base annotation class from which the concrete classes like AnnotationAffx, AnnotationEnvision etc. are derived


Annotation(cacheFolderName="", primaryColumn="From", secondaryColumn="To", swap=FALSE, species="Homo sapiens", verbose=FALSE, ...)



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


Primary column to be retrieved from a data frame obtained for a given service when getIdMap() on a given annotation object is called. Default is 'From'.


Secondary column(s) to be retrieved from a data frame obtained for a given service when getIdMap on a given annotation object is called. Default is 'To'.


A 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 FALSE.


A character vector or NA indicating if filtering of the results on a particular set of species should be performed if a given service provides the species information. If NA, no filtering is performed. Default is "Homo sapiens".


if TRUE enables diagnostic messages. Default is FALSE.


Additional parameters

Fields and Methods


getDataFrame Get the entire data set available from a particular service in a form of a data frame.
getFolderName Get caching folder name for a given Annotation object.
getIdMap Get an IdMap object using the data retrieved by a particular service represented by annotation object.
getServiceRoot Get a root directory for a particular annotation object.
setOptions Set the parameters for an annotation object.

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

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