AnnotationEnsemblCsv: The AnnotationEnsemblCsv class

Description

Package: Class AnnotationEnsemblCsv

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

Usage

AnnotationEnsemblCsv(cacheFolderName="EnsemblCsv", primaryColumn=c("UniProt.SwissProt.Accession", "UniProt.TrEMBL.Accession"), secondaryColumn=NA, swap=FALSE, full.merge=TRUE, df_filename=NULL, ...)

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.

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.

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.

...

Additional parameters, see Annotation.

Fields and Methods

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

Examples

Run this code

## Not run: 
#  Annotation$init();
#  #create Ensembl annotation object
#  annObj<-AnnotationEnsemblCsv(cacheFolderName="EnsemblCsv");
# ## End(Not run)

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