AnnotationEnsembl: The AnnotationEnsembl class

Description

Package: Class AnnotationEnsembl

Object ~~| ~~+--Annotation ~~~~~~~| ~~~~~~~+--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.

Usage

AnnotationEnsembl(cacheFolderName="Ensembl", primaryColumn=c("uniprot_swissprot_accession", "uniprot_sptrembl"), secondaryColumn=NA, swap=FALSE, species="hsapiens_gene_ensembl", full.merge=TRUE, ...)

Arguments

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 NA (default), the column name(s) derived automatically from the array type parameter during the getDataFrame() call. It should be noted that the probeset ID column name in Ensembl data format is array specific ('Affy.HG.U133.PLUS.2' for example) and therefore needs to be selected on per array basis if specified explicitely.

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.

species

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 'hsapiens_gene_ensembl'.

full.merge

A logical indicating which version of primary columns merging algorithm to use. If@ TRUE (default), all unique pairs and are generated, and if FALSE, only those pairs from for which Uniprot ID is not present in pairs are included.

...

Additional parameters, see Annotation.

Fields and Methods

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

Examples

Run this code

## Not run: 
#  Annotation$init();
#  #create Ensembl annotation object
#  annObj<-AnnotationEnsembl(species="hsapiens_gene_ensembl");
# ## End(Not run)

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