\name{xmapcore.coords}
\alias{genome.to.protein.coords}
\alias{genome.to.transcript.coords}
\alias{protein.coords.to.genome}
\alias{transcript.coords.to.genome}
\title{
  xmapcore co-ordinate mapping functions
}
\description{
  Functions to go between Genomic, Proteomic and Transcriptual co-ordinate systems.
}
\usage{
  transcript.coords.to.genome( transcript.ids, position=1, as.vector=TRUE, check.bounds=TRUE, truncate=TRUE )
  genome.to.transcript.coords( position, transcript.ids, as.vector=TRUE, check.bounds=TRUE )
  protein.coords.to.genome( protein.ids, position=1, as.vector=TRUE, check.bounds=TRUE, truncate=TRUE )
  genome.to.protein.coords( position, protein.ids, as.vector=TRUE, check.bounds=TRUE )
}
\arguments{
  \item{transcript.ids}{ A vector of transcript.ids (or a RangedData object of transcripts returned from another xmapcore function)}
  \item{position}{ The position of interest (either a genomic position for both of the \code{genome.to.xxx} methods,
  or a protein or transcript sequence position for the other two methods )}
  \item{as.vector}{ Should the returned data be in the form of a vector (if \code{TRUE}) or a RangedData object (if \code{FALSE}) }
  \item{check.bounds}{ If \code{TRUE}, any postion outside the range of the protein/transcript will cause a warning to be issued and \code{NA} returned. }
  \item{truncate}{ If \code{truncate=TRUE}, any lengths beyond the end of the transcript or protein will be set to the last residue}
  \item{protein.ids}{ A vector of protein.ids (or a RangedData object of proteins returned from another xmapcore function) }
}
\details{
  If called with \code{as.vector=FALSE}, all locations which were not found, or are not applicable will be dropped from the result.
  This is because \code{RangedData} objects cannot represent \code{NA} or missing values.
}
\seealso{
  \code{\link{xmapcore.to}}\cr
  \code{\link{xmapcore.details}}\cr
  \code{\link{xmapcore.all}}\cr
  \code{\link{xmapcore.range}}\cr
  \code{\link{xmapcore.filters}}\cr
}
\author{
  Tim Yates
}
\examples{
  if(interactive()) {
    # Get the gene for 'tp53'
    gene        = symbol.to.gene( 'tp53', as.vector=F )
    # And the transcripts for this gene
    transcripts = gene.to.transcript( symbol.to.gene( 'tp53' ) )
    # And the proteins for this transcript
    proteins    = transcript.to.protein( transcripts )

    # get the transcript coords for the transcripts of this gene, at the start of this gene
    genome.to.transcript.coords( start( gene ), transcripts )
    #Returns a vector:
    # ENST00000413465 ENST00000359597 ENST00000504290 ENST00000510385 ENST00000504937
    #            1018              NA              NA              NA              NA     
    # ENST00000269305 ENST00000455263 ENST00000420246 ENST00000445888 ENST00000396473
    #              NA              NA              NA              NA              NA     
    # ENST00000545858 ENST00000419024 ENST00000509690 ENST00000514944 ENST00000505014
    #              NA              NA              NA              NA              NA
    # ENST00000414315 ENST00000508793 ENST00000503591 
    #              NA              NA              NA

    # With as.vector=FALSE
    genome.to.transcript.coords( start( gene ), transcripts, as.vector=FALSE )
    # RangedData with 1 row and 1 value column across 1 space
    #             space       ranges | coord.space
    #       <character>    <IRanges> | <character>
    # 1 ENST00000413465 [1018, 1018] |  transcript

    genome.to.protein.coords( start( gene ), proteins )
    # ENSP00000410739 ENSP00000352610 ENSP00000269305 ENSP00000398846 ENSP00000391127
    #             340              NA              NA              NA              NA
    # ENSP00000391478 ENSP00000379735 ENSP00000437792 ENSP00000402130 ENSP00000425104
    #              NA              NA              NA              NA              NA
    # ENSP00000423862 ENSP00000394195 ENSP00000424104 ENSP00000426252 
    #              NA              NA              NA              NA 

    # With as.vector=FALSE
    genome.to.protein.coords( start( gene ), proteins, as.vector=FALSE )
    # RangedData with 1 row and 2 value columns across 1 space
    #             space     ranges |     frame coord.space
    #       <character>  <IRanges> | <numeric> <character>
    # 1 ENSP00000410739 [340, 340] |         0     protein
  }
}