AnnDbPkg-maker         package:AnnotationDbi         R Documentation

_C_r_e_a_t_e_s _a_n _S_Q_L_i_t_e-_b_a_s_e_d _a_n_n_o_t_a_t_i_o_n _p_a_c_k_a_g_e

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

     Creates an SQLite-based annotation package from an SQLite file.

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

       makeAnnDbPkg(x, dbfile, dest_dir=".", no.man=FALSE, ...)
       loadAnnDbPkgIndex(file)

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

       x: A AnnDbPkgSeed object, a list, a string or a regular
          expression. 

  dbfile: The path to the SQLite containing the annotation data for the
          package to build. 

dest_dir: The directory where the package will be created. 

    file: The path to a DCF file containing the list of annotation
          packages to build. 

  no.man: If 'TRUE' then no man page is included in the package. 

     ...: Extra args used for extra filtering. 

_S_e_e _A_l_s_o:

     AnnDbPkg-checker

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

       ## With a "AnnDbPkgSeed" object:
       seed <- new("AnnDbPkgSeed",
           Package="hgu133a2.db",
           Version="0.0.99",
           PkgTemplate="HUMANCHIP.DB",
           AnnObjPrefix="hgu133a2"
       )
       if (FALSE)
           makeAnnDbPkg(seed, "path/to/hgu133a2.sqlite")

       ## With package names:
       ## (Note that in this case makeAnnDbPkg() will use the package descriptions
       ## found in the master index file ANNDBPKG-INDEX.TXT located in the
       ## AnnotationDbi package.)
       if (FALSE)
           makeAnnDbPkg(c("hgu95av2.db", "hgu133a2.db"))

       ## A character vector of length 1 is treated as a regular expression:
       if (FALSE)
           makeAnnDbPkg("hgu.*")
       ## To make all the packages described in the master index:
       if (FALSE)
           makeAnnDbPkg("")
       ## Extra args can be used to narrow down the roaster of packages to make:
       if (FALSE) {
           makeAnnDbPkg("", PkgTemplate="HUMANCHIP.DB", manufacturer="Affymetrix")
           makeAnnDbPkg(".*[3k]\\.db", species=c("Mouse", "Rat"))
       }

       ## The master index file ANNDBPKG-INDEX.TXT can be loaded with:
       loadAnnDbPkgIndex()

