writeData_DB           package:PAnnBuilder           R Documentation

_P_a_r_s_e _a_n_d _W_r_i_t_e _D_a_t_a _i_n_t_o _R _D_a_t_a _P_a_c_k_a_g_e_s

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

     These functions store data tables in the "*.sqlite" file in
     SQLite-based  annotation package.

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

     createEmptyDPkg(pkgName, pkgPath,folders = c("man", "R", "data"), force = TRUE)

     writeMeta_DB(db, repList)

     writeData_DB(type, srcUrls, db, organism="")
     writeSPData_DB(srcUrls, db, organism)
     writeIPIData_DB(srcUrls, db, organism)
     writeREFSEQData_DB(srcUrls, db, organism)
     writeSYSBODYFLUIDData_DB(srcUrls, db)
     writeGOAData_DB(srcUrls, db)
     writeHomoloGeneData_DB(srcUrls, db)
     writeInParanoidData_DB(srcUrls, db)
     writeGENEINTData_DB(srcUrls, db)
     writeINTACTData_DB(srcUrls, db)
     writeMPPIData_DB(srcUrls, db)
     write3DIDData_DB(srcUrls, db)
     writeDOMINEData_DB(srcUrls, db)
     writePeptideAtlasData_DB(srcUrls, db)
     writeSYSPTMData_DB(srcUrls, db)
     writeSCOPData_DB(srcUrls, db)
     writeBACELLOData_DB(srcUrls, db)
     writeDBSUBLOCData_DB(srcUrls, db)

     writeName_DB(type, srcUrls, db)
     writeGOName_DB(srcUrls, db) 
     writeKEGGName_DB(srcUrls, db)
     writePFAMName_DB(srcUrls, db)
     writeINTERPROName_DB(srcUrls, db)
     writeTAXName_DB(srcUrls, db)

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

 pkgName: the name of the data package to be built. (e.g. "hsaSP") 

 pkgPath: a character string for the full path of an existing directory
          where the built backage will be stored.

 folders: a string vector for the file folder of establish R package.

   force: a boolean to indicate whether the existed homonymic folder 
          will be removed.

      db: a object that extends DBIConnection.

 repList: a named list which will replace the symbols in template file.

    type: character string, giving the name of concerned database.

 srcUrls: a character string, giving the url of the source file.

organism: a character string for the name of the organism of concern.
          (eg: "Homo sapiens")

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

     These functions download and parse data from diverse databases.
     The result files are stored as tables in the "*.sqlite" file.

     'writeMeta_DB' writes information from "repList" into a table 
     called "metadata".

     'writeData_DB' download and parse source file, and write the
     result files into tables.

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

     Hong Li

