popHUMANDB           package:AnnotationDbi           R Documentation

_P_o_p_u_l_a_t_e_s _a_n _S_Q_L_i_t_e _D_B _w_i_t_h _a_n_d _p_r_o_d_u_c_e_s _a _s_c_h_e_m_a _d_e_f_i_n_i_t_i_o_n

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

     Creates SQLite file useful for making a SQLite based annotation
     package.  Also produces the schema file which details the schema
     for the database produced.

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

       popHUMANDB(prefix, chipSrc, metaDataSrc, outputDir, printSchema)

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

  prefix: prefix is the first part of the eventual desired package
          name. (ie. "prefix.sqlite") 

 chipSrc: The path and filename to the intermediate database containing
          the annotation data for the sqlite to build. 

metaDataSrc: Either a named character vector containing pertinent
          information about the metadata OR the path and filename to
          the intermediate database containing the metadata information
          for the package.

          If this is a custom package, then it must be a named vector
          with the following fields:

          metaDataSrc <- c( DBSCHEMA="the DB schema", ORGANISM="the
          organism", SPECIES="the species", MANUFACTURER="the
          manufacturer", CHIPNAME="the chipName", MANUFACTURERURL="the
          manufacturerUrl")

outputDir: Where you would like the output files to be placed. 

printSchema: Boolean to indicate whether or not to produce an output of
          the schema (default is FALSE). 

_E_x_a_m_p_l_e_s:

     ## Not run: 
       ##Set up the metadata
       my_metaDataSrc <- c( DBSCHEMA="the DB schema",
                         ORGANISM="the organism",
                         SPECIES="the species",
                         MANUFACTURER="the manufacturer",
                         CHIPNAME="the chipName",
                         MANUFACTURERURL="the manufacturerUrl")  

       ##Builds the org.Hs.eg sqlite:
       popHUMANDB(prefix="org.Hs.eg",
                  chipSrc = "/mnt/cpb_anno/mcarlson/proj/sqliteGen/nli/annosrc/db/chipsrc_human.sqlite",
                  metaDataSrc = my_metaDataSrc,
                  printSchema=TRUE)

       ##Or if the package is a standard package (it probably isn't):
       ##Builds the org.Hs.eg sqlite:
       popHUMANDB(prefix="org.Hs.eg",
                  chipSrc = "/mnt/cpb_anno/mcarlson/proj/sqliteGen/nli/annosrc/db/chipsrc_human.sqlite",
                  metaDataSrc = "/mnt/cpb_anno/mcarlson/proj/sqliteGen/nli/annosrc/db/metadatasrc.sqlite",
                  printSchema=TRUE)
     ## End(Not run)

