\name{xmapcore.to}
\alias{xmapcore.to}
\alias{array.to.probeset}
\alias{domain.to.gene}
\alias{domain.to.probeset}
\alias{domain.to.protein}
\alias{domain.to.transcript}
\alias{est_exon.to.est_gene}
\alias{est_exon.to.est_transcript}
\alias{est_exon.to.probeset}
\alias{est_gene.to.est_exon}
\alias{est_gene.to.est_transcript}
\alias{est_gene.to.probeset}
\alias{est_transcript.to.est_exon}
\alias{est_transcript.to.est_gene}
\alias{est_transcript.to.probeset}
\alias{exon.to.gene}
\alias{exon.to.probeset}
\alias{exon.to.transcript}
\alias{gene.to.domain}
\alias{gene.to.exon}
\alias{gene.to.exon_probeset}
\alias{gene.to.probeset}
\alias{gene.to.protein}
\alias{gene.to.symbol}
\alias{gene.to.synonym}
\alias{gene.to.transcript}
\alias{prediction_transcript.to.prediction_exon}
\alias{prediction_transcript.to.probeset}
\alias{probe.to.hit}
\alias{probe.to.probeset}
\alias{probeset.to.cdnatranscript}
\alias{probeset.to.domain}
\alias{probeset.to.est_exon}
\alias{probeset.to.est_gene}
\alias{probeset.to.est_transcript}
\alias{probeset.to.exon}
\alias{probeset.to.gene}
\alias{probeset.to.hit}
\alias{probeset.to.prediction_transcript}
\alias{probeset.to.probe}
\alias{probeset.to.protein}
\alias{probeset.to.transcript}
\alias{protein.to.domain}
\alias{protein.to.gene}
\alias{protein.to.probeset}
\alias{protein.to.transcript}
\alias{symbol.to.est_gene}
\alias{symbol.to.est_transcript}
\alias{symbol.to.gene}
\alias{symbol.to.transcript}
\alias{synonym.to.est_gene}
\alias{synonym.to.est_transcript}
\alias{synonym.to.gene}
\alias{synonym.to.transcript}
\alias{transcript.to.cdnaprobeset}
\alias{transcript.to.domain}
\alias{transcript.to.exon}
\alias{transcript.to.exon_probeset}
\alias{transcript.to.gene}
\alias{transcript.to.probeset}
\alias{transcript.to.protein}
\alias{transcript.to.synonym}
\title{
  xmapcore \'to\' functions
}
\description{
  Map between the different levels of annotation in X:Map. For example, given a vector of gene identifiers, \code{gene.to.exon} 
  will return the exons in those genes.
}
\usage{
  array.to.probeset( ids, as.vector=TRUE )
  domain.to.gene( ids, as.vector=TRUE )
  domain.to.probeset( ids, as.vector=TRUE )
  domain.to.protein( ids, as.vector=TRUE )
  domain.to.transcript( ids, as.vector=TRUE )
  est_exon.to.est_gene( ids, as.vector=TRUE )
  est_exon.to.est_transcript( ids, as.vector=TRUE )
  est_exon.to.probeset( ids, as.vector=TRUE )
  est_gene.to.est_exon( ids, as.vector=TRUE )
  est_gene.to.est_transcript( ids, as.vector=TRUE )
  est_gene.to.probeset( ids, as.vector=TRUE )
  est_transcript.to.est_exon( ids, as.vector=TRUE )
  est_transcript.to.est_gene( ids, as.vector=TRUE )
  est_transcript.to.probeset( ids, as.vector=TRUE )
  exon.to.gene( ids, as.vector=TRUE )
  exon.to.probeset( ids, as.vector=TRUE )
  exon.to.transcript( ids, as.vector=TRUE )
  gene.to.domain( ids, as.vector=TRUE )
  gene.to.exon( ids, as.vector=TRUE )
  gene.to.exon_probeset( ids, probes.min=4 )
  gene.to.probeset( ids, as.vector=TRUE )
  gene.to.protein( ids, as.vector=TRUE )
  gene.to.symbol( ids )
  gene.to.synonym( ids, as.vector=TRUE )
  gene.to.transcript( ids, as.vector=TRUE )
  prediction_transcript.to.prediction_exon( ids )
  prediction_transcript.to.probeset( ids, as.vector=TRUE )
  probe.to.hit( ids )
  probe.to.probeset( ids, as.vector=TRUE )
  probeset.to.cdnatranscript( ids, as.vector=TRUE, rm.unreliable=TRUE )
  probeset.to.domain( ids, as.vector=TRUE, rm.unreliable=TRUE )
  probeset.to.est_exon( ids, as.vector=TRUE, rm.unreliable=TRUE )
  probeset.to.est_gene( ids, as.vector=TRUE, rm.unreliable=TRUE )
  probeset.to.est_transcript( ids, as.vector=TRUE, rm.unreliable=TRUE )
  probeset.to.exon( ids, as.vector=TRUE, rm.unreliable=TRUE )
  probeset.to.gene( ids, as.vector=TRUE, rm.unreliable=TRUE )
  probeset.to.hit( ids, rm.unreliable=TRUE )
  probeset.to.prediction_transcript( ids, as.vector=TRUE, rm.unreliable=TRUE )
  probeset.to.probe( ids, as.vector=TRUE )
  probeset.to.protein( ids, as.vector=TRUE, rm.unreliable=TRUE )
  probeset.to.transcript( ids, as.vector=TRUE, rm.unreliable=TRUE )
  protein.to.domain( ids, as.vector=TRUE )
  protein.to.gene( ids, as.vector=TRUE )
  protein.to.probeset( ids, as.vector=TRUE )
  protein.to.transcript( ids, as.vector=TRUE )
  symbol.to.est_gene( ids, as.vector=TRUE )
  symbol.to.est_transcript( ids, as.vector=TRUE )
  symbol.to.gene( ids, as.vector=TRUE )
  symbol.to.transcript( ids, as.vector=TRUE )
  synonym.to.est_gene( ids, as.vector=TRUE )
  synonym.to.est_transcript( ids, as.vector=TRUE )
  synonym.to.gene( ids, as.vector=TRUE )
  synonym.to.transcript( ids, as.vector=TRUE )
  transcript.to.cdnaprobeset( ids, as.vector=TRUE )
  transcript.to.domain( ids, as.vector=TRUE )
  transcript.to.exon( ids, as.vector=TRUE )
  transcript.to.exon_probeset( ids, probes.min=4 )
  transcript.to.gene( ids, as.vector=TRUE )
  transcript.to.probeset( ids, as.vector=TRUE )
  transcript.to.protein( ids, as.vector=TRUE )
  transcript.to.synonym( ids, as.vector=TRUE )
}
\arguments{
  \item{as.vector}{ If \code{TRUE} returns a vector of database identifiers. If \code{FALSE} returns a \code{link{RangedData}} object containing detailed annotation. }
  \item{ids}{ Database identifiers to map from. Can be either a vector of database indentifiers, or a \code{\link{RangedData}} object.}
  \item{probes.min}{ How many probes need to match before the probeset is returned. }
  \item{rm.unreliable}{ If \code{TRUE}, the input probeset list is filtered, and all unreliable probesets are removed. }
}
\details{
  In most cases, these functions should be self-explantory. However, by default, the mappings involving probes and probesets 
  do some filtering of the data. This means that probesets which have one or more probes that don't match to the genome, or which 
  match to multiple loci, are removed (see \code{\link{unreliable}} for more details).
}
\value{
  Results in an \code{\link{RangedData}} object, one \'row\' per feature, containing detailed annotations, or a \code{vector}, as defined by \code{as.vector}.

}
\seealso{
  \code{\link{xmapcore.details}}\cr
  \code{\link{xmapcore.all}}\cr
  \code{\link{xmapcore.range}}\cr
  \code{\link{xmapcore.utils}}\cr
  \code{\link{xmapcore.filters}}\cr
  \code{link{RangedData}}
}
\author{
  Tim Yates
}
\examples{
  if(interactive()) {
    xmap.connect()
    gene.to.exon(symbol.to.gene("TP53"))
  } 
}