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("db", "env"))

_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, and then the default value of
          'type' takes over.

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

     'getAnnMap' uses the search path (see 'search') to find an
     appropriate annotation data package; when called with
     'chip="hgu95av2"', the function will use the first hgu95av2
     package on the search path whether it be db or environment-based. 
     If 'load=TRUE' and no suitable package is found on the search
     path, then the function will attempt to load an appropriate
     package.  The 'type' argument is used to determine which type of
     package (db or env) is loaded first.

_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.

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

     Seth Falcon

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

     map <- getAnnMap("ENTREZID", "hgu95av2", load=TRUE, type=c("env", "db"))
     class(map)

