getAnnMap              package:annotate              R Documentation

_G_e_t _a_n_n_o_t_a_t_i_o_n _m_a_p

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

     This function retrieves a map object from an annotation data
     package.  It is intended to serve as a common interface for
     obtaining map objects from both SQLite-based and environment-based
     annotation data packages.

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

     getAnnMap(map, chip, load = TRUE, type = c("env", "db"))

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

     map: a string specifying the name of the map to retrieve.  For
          example, '"ENTREZID"' or '"GO"'

    chip: a string describing the chip or genome

    load: a logical value.  When 'TRUE', 'getAnnMap' will try to load
          the annotation data package if it is not already attached.

    type: a character vector of one or more annotation data package
          types.  The currently supported types are '"db"' and '"env"'.
           If 'load' is 'TRUE', you can specify both '"db"' and '"env"'
          and the order will determine which type is tried first.  This
          provides a fall-back mechanism when the preferred annotation
          data package type is not available.  If 'type' is missing,
          then the first matching annotation package found in the
          search path will be used.

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

     'getAnnMap' expects the annotation data package to be loaded and
     attached.  If 'load' is TRUE, the package will be attached.

_V_a_l_u_e:

     If 'type' is '"db"', an S4 object representing the requested map. 
     If 'type' is '"env"', an R 'environment' object representing the
     requested map.

_W_a_r_n_i_n_g:

     SQLite-based annotation data packages are planned for the BioC 2.1
     release.  Use of 'type="db"' may not work as desired in this
     release.  In the next release, the order of '"env"' and '"db"'
     will be reversed to give preference to the SQLite-based packages.

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

     Seth Falcon

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

     map <- getAnnMap("ENTREZID", "hgu95av2")
     class(map)

