Description Usage Arguments Fields and Methods Author(s) Examples
Package:
Class AnnotationEnsemblCsv
Object
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Annotation
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AnnotationEnsembl
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AnnotationEnsemblCsv
Directly known subclasses:
public static class AnnotationEnsemblCsv
extends AnnotationEnsembl
The AnnotationEnsemblCsv class encapsulates the functionality allowing to retrieve data from the Ensembl intercative online query system. The ID matching information fitered on species and the microarray chip type is retrieved as comma delimited csv file. The AnnotationEnsemblCsv object encapsulates the functionality allowing to interactively choose the Ensembl query results csv file and convert it into a data frame during the getIdMap() and getDataFrame() calls on the AnnotationEnsemblCsv object.
1 |
cacheFolderName |
The symbolic name of a service represented by a given AnnotationEnsembl object. |
primaryColumn |
Primary column(s) to be retrieved from a data frame obtained from the Ensembl csv file when getIdMap() is called. As the Ensembl returns the match results for SwissProt and Tremb accessions in separate columns, it is possible to retrieve either or them or merge them together by explicetely specifying the set of columns to be merged. Default is c('uniprot_swissprot_accession','uniprot_sptrembl'). |
secondaryColumn |
secondaryColumn Secondary column (containing probeset IDs) to be retrieved from a data frame obtained from the Ensembl csv file
when getIdMap() is called. If |
swap |
A |
full.merge |
A |
df_filename |
Character string or NULL. In the first case the character string contains the name of conversion results file and in the second case the file name is determined interactively through the Open File dialog during the call to Annotation.getIdMap() or Annotation.getDataFrame() on the AnnotationEnsemblCsv object. |
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Additional parameters, see |
Methods:
No public methods defined.
Methods inherited from AnnotationEnsembl:
getColumns, getColumns1, getColumns2, readDF
Methods inherited from Annotation:
getArrayType, getArrayTypes, getColumns, getCredentials, getDataFrame, getFolderName, getIdMap, getRoot, getServiceRoot, init, readDF, setCredentials, setOptions
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clone, detach, equals, extend, finalize, gc, getEnvironment, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, objectSize, print, registerFinalizer, save
Alex Lisovich, Roger Day
1 2 3 4 5 6 | ## Not run:
Annotation$init();
#create Ensembl annotation object
annObj<-AnnotationEnsemblCsv(cacheFolderName="EnsemblCsv");
## End(Not run)
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