lumiMouseIDMapping_nuID  package:lumiMouseIDMapping  R Documentation

_M_a_p_p_i_n_g _n_u_I_D_s _o_f _I_l_l_u_m_i_n_a _M_o_u_s_e _c_h_i_p_s _t_o _t_h_e _m_o_s_t _r_e_c_e_n_t _M_u_s _m_u_s_c_u_l_u_s _R_e_f_S_e_q _r_e_l_e_a_s_e

_D_e_s_c_r_i_p_t_i_o_n:

     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.

_U_s_a_g_e:

       lumiMouseIDMapping_nuID()

_D_e_t_a_i_l_s:

     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).

_V_a_l_u_e:

     'lumiMouseIDMapping_nuID' returns a nuID mapping summary of
     Illumina Mouse chips.

_R_e_f_e_r_e_n_c_e_s:

     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).

_E_x_a_m_p_l_e_s:

       ## List the fields in the nuID_MappingInfo table
       conn <- lumiMouseIDMapping_dbconn()
       dbListFields(conn, 'nuID_MappingInfo')

       ## Summary of nuID mapping
       lumiMouseIDMapping_nuID()

