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\name{AnnotationEnsemblCsv}
\docType{class}
\alias{AnnotationEnsemblCsv}


\title{The AnnotationEnsemblCsv class}

\description{
 Package:   \cr
\bold{Class AnnotationEnsemblCsv}\cr

\code{\link[R.oo]{Object}}\cr
\code{~~|}\cr
\code{~~+--}\code{\link{Annotation}}\cr
\code{~~~~~~~|}\cr
\code{~~~~~~~+--}\code{\link{AnnotationEnsembl}}\cr
\code{~~~~~~~~~~~~|}\cr
\code{~~~~~~~~~~~~+--}\code{AnnotationEnsemblCsv}\cr

\bold{Directly known subclasses:}\cr
\cr

public static class \bold{AnnotationEnsemblCsv}\cr
extends \link{AnnotationEnsembl}\cr



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{
\item{cacheFolderName}{ The symbolic name of a service represented by a given AnnotationEnsembl object.}
\item{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').}
\item{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 \code{\link[base]{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.}
\item{swap}{ A \code{\link[base]{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 \code{\link[base:logical]{TRUE}}.}
\item{full.merge}{ A \code{\link[base]{logical}} indicating which version of primary columns merging algorithm to use. If@ TRUE (default), all unique pairs
<probeset ID, SwissProt> and <probeset ID, Trembl> are generated, and if \code{\link[base:logical]{FALSE}}, only those pairs from <probeset ID, Trembl>
for which Uniprot ID is not present in <probeset ID, SwissProt> pairs are included.}
\item{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.}
\item{...}{Additional parameters, see \code{\link{Annotation}}.}
}

\examples{
\dontrun{
 Annotation$init();
 #create Ensembl annotation object
 annObj<-AnnotationEnsemblCsv(cacheFolderName="EnsemblCsv");
}}

\section{Fields and Methods}{
 \bold{Methods:}\cr
\emph{No public methods defined}.


 \bold{Methods inherited from AnnotationEnsembl}:\cr
getColumns, getColumns1, getColumns2, readDF

 \bold{Methods inherited from Annotation}:\cr
getArrayType, getArrayTypes, getColumns, getCredentials, getDataFrame, getFolderName, getIdMap, getRoot, getServiceRoot, init, readDF, setCredentials, setOptions

 \bold{Methods inherited from Object}:\cr
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clone, detach, equals, extend, finalize, gc, getEnvironment, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, objectSize, print, registerFinalizer, save


}

\author{Alex Lisovich, Roger Day}
\keyword{classes}