\HeaderA{nuID2IlluminaID}{Matching nuIDs to Illumina IDs based on Illumina ID mapping library}{nuID2IlluminaID}
\keyword{methods}{nuID2IlluminaID}
\keyword{utilities}{nuID2IlluminaID}
\begin{Description}\relax
Matching nuIDs to Illumina IDs based on Illumina ID mapping library
\end{Description}
\begin{Usage}
\begin{verbatim}
nuID2IlluminaID(nuID, lib.mapping=NULL, species = c("Human", "Mouse", "Rat", "Unknown"), idType=c('All', 'Probe', 'Gene', 'Accession', 'Search_key', 'Symbol'), chipVersion = NULL, ...)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{nuID}] a vector of nuIDs 
\item[\code{lib.mapping}] the ID mapping library. If it is provided, the parameter "species" will be ignored. 
\item[\code{species}] the species of the chip designed for. If users do not know it, it can be set as "Unknown".
\item[\code{idType}] the Illumina ID type
\item[\code{chipVersion}] chipVersion information returned by function \code{\LinkA{getChipInfo}{getChipInfo}} 
\item[\code{...}] other parameters of \code{\LinkA{getChipInfo}{getChipInfo}} 
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
The parameter "idType" represents different types of Illumina IDs. It returns the entire table when idType = "All". When idType = 'Probe', it returns "ProbeId" or "Probe\_Id". When idType = 'Gene', it returns "Target" or "ILMN\_Gene" IDs.

This function basically returned the "idMapping" item returned by function \code{\LinkA{getChipInfo}{getChipInfo}}.
If nuID is NULL and chipVersion is provided, it will return all mapping information of the chip.
\end{Details}
\begin{Value}
The mapping information from nuID to Illumina ID. It will be a matrix with each column corresponding to one matched manifest file when parameter "returnAllMatches" is TRUE. In this case, the columns are sorted from the best match to worst.
\end{Value}
\begin{Author}\relax
Pan Du
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{getChipInfo}{getChipInfo}}, \code{\LinkA{IlluminaID2nuID}{IlluminaID2nuID}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
        ## load example data
        data(example.lumi)
        nuIDs <- featureNames(example.lumi)
        if (require(lumiHumanIDMapping)) {
                illuminaID <- nuID2IlluminaID(nuIDs[1:5], lib='lumiHumanIDMapping')
                illuminaID
        }
\end{ExampleCode}
\end{Examples}

