nuID2IlluminaID             package:lumi             R Documentation

_M_a_t_c_h_i_n_g _n_u_I_D_s _t_o _I_l_l_u_m_i_n_a _I_D_s _b_a_s_e_d _o_n _I_l_l_u_m_i_n_a _I_D _m_a_p_p_i_n_g _l_i_b_r_a_r_y

_D_e_s_c_r_i_p_t_i_o_n:

     Matching nuIDs to Illumina IDs based on Illumina ID mapping
     library

_U_s_a_g_e:

     nuID2IlluminaID(nuID, lib.mapping=NULL, species = c("Human", "Mouse", "Rat", "Unknown"), idType=c('All', 'Probe', 'Gene', 'Accession', 'Search_key', 'Symbol'), chipVersion = NULL, ...)

_A_r_g_u_m_e_n_t_s:

    nuID: a vector of nuIDs 

lib.mapping: the ID mapping library. If it is provided, the parameter
          "species" will be ignored. 

 species: the species of the chip designed for. If users do not know
          it, it can be set as "Unknown".

  idType: the Illumina ID type

chipVersion: chipVersion information returned by function 'getChipInfo' 

     ...: other parameters of 'getChipInfo' 

_D_e_t_a_i_l_s:

     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 'getChipInfo'. If nuID is NULL and chipVersion is
     provided, it will return all mapping information of the chip.

_V_a_l_u_e:

     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.

_A_u_t_h_o_r(_s):

     Pan Du

_S_e_e _A_l_s_o:

     'getChipInfo', 'IlluminaID2nuID'

_E_x_a_m_p_l_e_s:

             ## load example data
             data(example.lumi)
             nuIDs <- featureNames(example.lumi)
             if (require(lumiHumanIDMapping)) {
                     illuminaID <- nuID2IlluminaID(nuIDs[1:5], lib='lumiHumanIDMapping')
                     illuminaID
             }

