Annotation: The Annotation class

In professorbeautiful/IdMappingRetrieval: ID Mapping Data Retrieval

Description

Package:
Class Annotation

Object
~~|
~~+--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

Usage

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

Arguments

cacheFolderName	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'
primaryColumn	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'.
secondaryColumn	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'.
swap	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.
species	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".
verbose	if TRUE enables diagnostic messages. Default is FALSE.
...	Additional parameters

Fields and Methods

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

Author(s)

Alex Lisovich, Roger Day

professorbeautiful/IdMappingRetrieval documentation built on May 26, 2019, 8:33 a.m.