AnnotationNetAffx: The AnnotationNetAffx class

In professorbeautiful/IdMappingRetrieval: ID Mapping Data Retrieval

Description

Package:
Class AnnotationNetAffx

Object
~~|
~~+--Annotation
~~~~~~~|
~~~~~~~+--AnnotationAffx
~~~~~~~~~~~~|
~~~~~~~~~~~~+--AnnotationNetAffx

Directly known subclasses:

public static class AnnotationNetAffx
extends AnnotationAffx

The AnnotationNetAffx class encapsulates the functionality allowing to retrieve data from the NetAffx batch query system through the Annotation.getIdMap() and Annotation.getDataFrame() calls on this object. The NetAffx batch query system requires to submit the probeset IDs by providing text files in a special format, maximum 10000 IDs per file. The results are returned in a form of a tab delimited text file, one file per submission, so the query results for a whole array are presented by a set of such files. The AnnotationNetAffx object encapsulates the functionality allowing to interactively choose the set of result files and merge them into a single data frame during the Annotation.getIdMap() and Annotation.getDataFrame() calls on the AnnotationNetAffx object.

Usage

AnnotationNetAffx(cacheFolderName="NetAffxCsv", primaryColumn="Probe.Set.ID", secondaryColumn="SwissProt", swap=TRUE, df_filename=NULL, ...)

Arguments

cacheFolderName	The symbolic name of a service represented by a given AnnotationNetAffx object.
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	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 TRUE.
df_filename	Character vector, character string or NULL. In the first case the character vector contains the names of a resulting file set, in the second, the character string contains the name of directory in which the files are stored, and in the third the file set is determined interactively through the Open File dialog during the call to getIdMap() or getDataFrame() on the AnnotationAffxCsv object.
...	Additiional parameters, see Annotation.

Fields and Methods

Methods:

Methods inherited from AnnotationAffx:
getColumns, getProbesetList, readDF, setCredentials

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

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