createAnnObjs          package:PAnnBuilder          R Documentation

_C_r_e_a_t_e_s _t_h_e _A_n_n_O_b_j _i_n_s_t_a_n_c_e_s

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

     These functions creates the AnnObj instances for the SQLite-based
     annotation  data packages.

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

     createSeeds(type) 

     createAnnObjs(type, prefix, datacache, dbconn)

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

    type: character string, giving the name of concerned database.
          Possible  values of type are : "sp", "trembl", "ipi",
          "refseq", "geneint", "intact", "mppi",  "3DID", "DOMINE",
          "BaCelLo", "DBSubLoc", "SCOP", "HomoloGene", "InParanoid", 
          "PeptideAtlas", "SysPTM", "SysBodyFluid", "GOA", "GO",
          "KEGGNAME", "PFAMNAME",  "INTERPRONAME", "TAXNAME", "dName",
          "cross", "pSeq"

  prefix: the prefix of the name of the data package to be built. (e.g.
           "hsaSP"). The name of builded package is prefix+".db". 

datacache: a R environment, giving the name of "*.sqlite" database
          file,  and a object which extends DBIConnection to the
          database.

  dbconn: a connection object to the package.

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

     Given the abbreviation of databases, 'createSeeds' returns a list 
     which describes the set of AnnObj objects.

     'createAnnObjs' creates the AnnObj instances based on the values 
     of 'createSeeds'.

     'dbschema(x, file="", show.indices=FALSE)': Print the schema
     definition of the SQLite DB. Also works if 'x' is a DBIConnection
     object. The  'file' argument must be a connection, or a character
     string naming the  file to print to (see the 'file' argument of
     the 'cat'  function for the details). The CREATE INDEX statements
     are not shown by default. Use 'show.indices=TRUE' to get them.

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

     Hong Li

