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