nuID2RefSeqID              package:lumi              R Documentation

_M_a_p _n_u_I_D _t_o _R_e_f_S_e_q _I_D

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

     Map nuID to RefSeq ID based on IDMapping libraries.

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

     nuID2RefSeqID(nuID = NULL, lib.mapping, filterTh = c(Strength1 = 95, Uniqueness = 95), returnAllInfo = FALSE)

_A_r_g_u_m_e_n_t_s:

    nuID: a vector of nuIDs. If it is NULL, all mappings will be
          returned. 

lib.mapping: the ID mapping library 

filterTh: the mapping quality filtering threshold used to filter the ID
          mapping. 

returnAllInfo: determine to return the detailed mapping information or
          just the matched RefSeq IDs 

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

     This function is based on the return of 'getNuIDMappingInfo'
     function. It uses mapping quality information to filter out the
     bad mappings. The names of "filterTh" are basically the field
     names of "nuID_MappingInfo" table, which include 'Strength1',
     'Strength2', 'Uniqueness' and 'Total hits'. For the definition of
     these metrics, please refer to the IDMapping library or see the
     reference website.

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

     returns the matched RefSeq IDs or a data.frame with each row
     corresponding to an input nuID (when "returnAllInfo" is TRUE).

_A_u_t_h_o_r(_s):

     Warren Kibbe, Pan Du, Simon Lin

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

     https://prod.bioinformatics.northwestern.edu/nuID/

_S_e_e _A_l_s_o:

     See Also 'getNuIDMappingInfo'

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

             ## load example data
             data(example.lumi)
             if (require(lumiHumanIDMapping)) {
                     nuIDs <- featureNames(example.lumi)
                     mappingInfo <- nuID2RefSeqID(nuIDs, lib.mapping='lumiHumanIDMapping')
                     head(mappingInfo)
             }

