lumiHumanIDMapping_nuID  package:lumiHumanIDMapping  R Documentation

_M_a_p_p_i_n_g _n_u_I_D_s _o_f _I_l_l_u_m_i_n_a _H_u_m_a_n _c_h_i_p_s _t_o _t_h_e _m_o_s_t _r_e_c_e_n_t _H_o_m_o _s_a_p_i_e_n_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 Human chips by BLASTing each probe
     sequence (converted from nuID) against the the most recent Homo
     sapiens RefSeq release. The mapping also includes the mapping
     quality information, like mapping strength, uniqueness, number of
     hits.

_U_s_a_g_e:

       lumiHumanIDMapping_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:

     'lumiHumanIDMapping_nuID' returns a nuID mapping summary of
     Illumina Human 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 <- lumiHumanIDMapping_dbconn()
       dbListFields(conn, 'nuID_MappingInfo')

       ## Summary of nuID mapping
       lumiHumanIDMapping_nuID()

