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)

