nuID2EntrezID              package:lumi              R Documentation

_M_a_p _n_u_I_D _t_o _E_n_t_r_e_z _I_D

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

     Map nuID to EntrezID through RefSeq ID based on IDMapping
     libraries.

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

     nuID2EntrezID(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. The mapping from nuID to EntrezID was based on the
     mapping from nuID to RefSeqID and RefSeqID to EntrezID. It uses
     mapping quality information to filter out the bad mappings from
     nuID to RefSeqID. 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 Entrez 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 <- nuID2EntrezID(nuIDs, lib.mapping='lumiHumanIDMapping')
                     head(mappingInfo)
             }

