popHUMANCHIPDB         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:

       popHUMANCHIPDB(affy, prefix, fileName, chipMapSrc, chipSrc, metaDataSrc,
       otherSrc, baseMapType, outputDir, printSchema)

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

    affy: Boolean to indicate if this is starting from an affy csv file
          or not.  If it is, then that will be parsed to make the
          sqlite file, if not, then you can feed a tab delimited file
          with IDs as was done before with AnnBuilder. 

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

fileName: The path and filename for the file to be parsed.  This can
          either be an affy csv file or it can be a more classic file
          type. 

chipMapSrc: The path and filename to the intermediate database
          containing the mapping data for allowed ID types and how
          these IDs relate to each other.     

 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")

otherSrc: The path and filenames to any other lists of IDs which might
          add information about how a probe will map. 

baseMapType: The type of ID that is used in the initial base mapping. 
          This would be the ID type present in the fileName. 

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:
       popHUMANCHIPDB(affy=TRUE,
                      prefix="hgu95av2",
                      fileName="/mnt/cpb_anno/mcarlson/proj/sqliteGen/srcFiles/hgu95av2/HG_U95Av2_annot.csv.070824",
                      chipMapSrc = "/mnt/cpb_anno/mcarlson/proj/sqliteGen/nli/annosrc/db/chipmapsrc_human.sqlite",
                      chipSrc = "/mnt/cpb_anno/mcarlson/proj/sqliteGen/nli/annosrc/db/chipsrc_human.sqlite",
                      metaDataSrc = my_metaDataSrc,
                      otherSrc=c(
                        EA="/mnt/cpb_anno/mcarlson/proj/sqliteGen/srcFiles/hgu95av2/hgu95av2.EA.txt",
                        UMICH="/mnt/cpb_anno/mcarlson/proj/sqliteGen/srcFiles/hgu95av2/hgu95av2_UMICH.txt"),
                      printSchema=TRUE)

       ##Or if the package is a standard package (it probably isn't):
       popHUMANCHIPDB(affy=TRUE,
                      prefix="hgu95av2",
                      fileName="/mnt/cpb_anno/mcarlson/proj/sqliteGen/srcFiles/hgu95av2/HG_U95Av2_annot.csv.070824",
                      chipMapSrc = "/mnt/cpb_anno/mcarlson/proj/sqliteGen/nli/annosrc/db/chipmapsrc_human.sqlite",
                      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",
                      otherSrc=c(
                        EA="/mnt/cpb_anno/mcarlson/proj/sqliteGen/srcFiles/hgu95av2/hgu95av2.EA.txt",
                        UMICH="/mnt/cpb_anno/mcarlson/proj/sqliteGen/srcFiles/hgu95av2/hgu95av2_UMICH.txt"),
                      printSchema=TRUE)
     ## End(Not run)

