getChipInfo               package:lumi               R Documentation

_G_e_t _I_l_l_u_m_i_n_a _C_h_i_p _I_n_f_o_r_m_a_t_i_o_n _b_a_s_e_d _o_n _p_r_o_b_e _i_d_e_n_t_i_f_i_e_r_s

_D_e_s_c_r_i_p_t_i_o_n:

     Retrieve the matched Illumina chip information by searching the
     provided probe identifiers through the Illumina identifiers in all
     manifest files.

_U_s_a_g_e:

     getChipInfo(x, lib.mapping = NULL, species = c("Human", "Mouse", "Rat", "Unknown"), chipVersion = NULL, idMapping = FALSE, returnAllMatches = FALSE, verbose = TRUE)

_A_r_g_u_m_e_n_t_s:

       x: a vector of probe identifiers, ExpressionSet object or a
          matrix with probe identifiers as row names 

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

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

chipVersion: chipVersion information returned by function 'getChipInfo' 

idMapping: determine whether return the idMapping information (between
          Illumina ID and nuID) 

returnAllMatches: determine whether return all matches or just the best
          match 

 verbose: determine whether print some warning information 

_D_e_t_a_i_l_s:

     The function searches the provided probe Identifiers (Illumina IDs
     or nuIDs) through all the manifest file ID information kept in the
     IDMapping libraries (lumiHumanIDMapping, lumiMouseIDMapping,
     lumiRatIDMapping). The Illumina IDs kept in the library include
     "Search_key" ("Search_Key"), "Target" ("ILMN_Gene"), "Accession",
     "Symbol", "ProbeId" ("Probe_Id"). To determine the best match, the
     function calculate the number of matched probes. The higher
     "matchedProbeNumber" is claimed as better. When the
     "matchedProbeNumber" is the same, the manifest file with fewer
     probes is claimed as better. If x is NULL and chipVersion is
     provided, it will return the entire mapping table of the chip.

_V_a_l_u_e:

     The function returns a list with following items: 

chipVersion: the file name of the manifest file for the corresponding
          version and release

 species: the species of the chip designed for

  IDType: the type of probe identifier

chipProbeNumber: the number of probes in the manifest file

matchedProbeNumber: the number of input probes matching the manifest
          file

idMapping: id mapping information between Illumina ID and nuID

     When parameter "returnAllMatches" is TRUE, the items of
     "chipVersion", "IDType", "chipProbeNumber", "inputProbeNumber",
     "matchedProbeNumber" will be a vector corresponding to the matched
     manifest files, whose "matchedProbeNumber" is larger than zero,
     and the "idMapping" will be a matrix with each column
     corresponding to one matched manifest file. All of the items are
     sorted from the best match to worst (The higher
     "matchedProbeNumber" is claimed as better. When the
     "matchedProbeNumber" is the same, the manifest file with fewer
     probes is claimed as better.).

_A_u_t_h_o_r(_s):

     Pan Du

_S_e_e _A_l_s_o:

     'nuID2IlluminaID', 'IlluminaID2nuID'

_E_x_a_m_p_l_e_s:

             ## load example data
             data(example.lumi)
             if (require(lumiHumanIDMapping)) {
                     chipInfo <- getChipInfo(example.lumi, species='Human')
                     chipInfo
             }

