\HeaderA{lumiMouseIDMapping\_nuID}{Mapping nuIDs of Illumina Mouse chips to the most recent Mus musculus RefSeq release}{lumiMouseIDMapping.Rul.nuID}
\keyword{utilities}{lumiMouseIDMapping\_nuID}
\keyword{datasets}{lumiMouseIDMapping\_nuID}
\begin{Description}\relax
We mapped nuIDs of Illumina Mouse chips by BLASTing each probe sequence (converted from nuID) against the the most recent Mus musculus RefSeq release. The mapping also includes the mapping quality information, like mapping strength, uniqueness, number of hits.
\end{Description}
\begin{Usage}
\begin{verbatim}
  lumiMouseIDMapping_nuID()
\end{verbatim}
\end{Usage}
\begin{Details}\relax
The nuID mapping information is kept in the nuID\_MappingInfo table in the ID Mapping library. The nuID mapping table includes following fields (columns):

1.      nuID: nuID for the probe sequence

2.      Refseq: The refseq IDs with perfect matching with probe sequence. If there are more than one refseq IDs, they are separated by ",".

3.      EntrezID: The Entrez gene IDs correspond to the refseq IDs. If there are more than one Entrez gene IDs, they are separated by ",". 

4.      Total\_hits\_of\_EntrezID: The number of unique Entrez gene IDs matched with the probe sequence.

5.  Refseq\_old: the refseq ID provided by Illumina company


Procedures of nuID mappings:

Briefly, we first mapped each probe sequence (converted from nuID) against the corresponding RefSeq sequence. Only perfect mapping will be considered. When one probe maps to multiple Refseq sequences, we will further check whether these Refseq sequences correspond to the same Entrez gene. To make sure the probes have unique mapping, we only consider the probe sequences mapped to a single Entrez Gene when we build the lumi annotation packages (lumiHumanAll.db, lumiMouseAll.db and lumiRatAll.db).
\end{Details}
\begin{Value}
\code{lumiMouseIDMapping\_nuID} returns a nuID mapping summary of Illumina Mouse chips.
\end{Value}
\begin{References}\relax
1. Du, P., Kibbe, W.A. and Lin, S.M., "nuID: A universal naming schema of oligonucleotides for Illumina, Affymetrix, and other microarrays", Biology Direct 2007, 2:16 (31May2007).
\end{References}
\begin{Examples}
\begin{ExampleCode}
  ## List the fields in the nuID_MappingInfo table
  conn <- lumiMouseIDMapping_dbconn()
  dbListFields(conn, 'nuID_MappingInfo')

  ## Summary of nuID mapping
  lumiMouseIDMapping_nuID()

\end{ExampleCode}
\end{Examples}

