Description Usage Arguments Fields and Methods Author(s) Examples
Package:
Class AnnotationEnsembl
Object
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Annotation
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AnnotationEnsembl
Directly known subclasses:
AnnotationEnsemblCsv
public static class AnnotationEnsembl
extends Annotation
The AnnotationEnsembl class encapsulates the functionality allowing to retrieve data from the Ensembl BioMart online query system using biomaRt R package through the Annotation.getIdMap() and Annotation.getDataFrame() calls on this 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 |
species |
Character vector or |
full.merge |
A |
... |
Additional parameters, see |
Methods:
No public methods defined.
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<-AnnotationEnsembl(species="hsapiens_gene_ensembl");
## End(Not run)
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