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)
             }

