zzz-NetAffxCompatibility-classpackage:AffyCompatibleR Documentation

(_A_u_t_o-_g_e_n_e_r_a_t_e_d) _c_l_a_s_s_e_s _a_n_d _m_e_t_h_o_d_s _f_o_r _n_a_v_i_g_a_t_i_n_g _N_e_t_A_f_f_x _r_e_s_o_u_r_c_e_s

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

     These classes and methods facilitate navigation of the NetAffx
     resource data base.  They are R representations of the Affymetrix
     classes defined in NetAffxAnnotFileList.dtd. The 'show' methods
     for these classs indicate how objects are to be accessed; details
     are in the `Annotations with NetAffx' vignette.

     The auto-generated classes are discoverable as indicated in the
     example below.

_O_b_j_e_c_t_s _f_r_o_m _t_h_e _C_l_a_s_s:

     Objects are created internally, by parsing XML retrieved from the
     local NetAffx data base or from the Affymetrix web site.

_S_l_o_t_s:

     Objects have a variety of slots. To discover slot names and
     content type, see the 'slotNames' portion of the example, below.

_E_x_t_e_n_d_s:

     Class '"NetAffxCompatibility"', directly. Class
     '"AffyCompatible"', by class "NetAffxCompatibility", distance 2.

_M_e_t_h_o_d_s:

     'Read' methods are defined on auto-generated classes to access
     slot content.

     Accessors are apparent from displaying the object; each line of
     the display is of the form 'accessor: content'. To retrieve the
     content of an instance 'object', invoke 'accessor(object)'.

     Some objects contains several instances of another object. These
     'typed associations' are represented by the '.TypedAssociation'
     class, and are navigated or subset as one would a standard R
     vector, e.g., using '[', '[['. A useful paradigm for displaying
     all instances is illustrated on the 'NetAffxResource' page.

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

     Martin Morgan <mtmorgan@fhcrc.org>

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

     Vignette `Annotations with NetAffx'. Affymetrix user login site
     <URL: https://www.affymetrix.com/site/login/login.affx>.

     'NetAffxResource' for creating and managing the NetAffx data base.

     'NetAffxResource' for navigating the data base.

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

     ## defined and auto-generated classes
     getClass("NetAffxCompatibility", where=getNamespace("AffyCompatible"))

     ## slots of an auto-generated class
     getSlots(getClass("AffxNetAffxAnnotFileList",
         where=getNamespace("AffyCompatible")))

     ## Not run: 
     example("NetAffxrResource-class")
     ## End(Not run)

