zzz-ARRCompatibility-class  package:AffyCompatible  R 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 _A_R_R _s_a_m_p_l_e
_a_t_t_r_i_b_u_t_e_s.

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

     These classes and methods facilitate navigation of the Affymetrix
     ARR sample attribute files. ARR files are generated by the
     Affymetrix AGCC (GeneChip\textregistered{} Command Console)
     application. Specifically, the classes are R representations of
     the Affymetrix classes defined in ArraySetAndTemplateFile.dtd. The
     'show' methods for these classs indicate how objects are to be
     accessed; details are in the `Retrieving MAGE and ARR sample
     attributes' vignette.

_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 ARR,
     and are not created directly by the user.

_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 '"ARRCompatibility"', directly. Class '"AffyCompatible"', by
     class "ARRCompatibility", distance 2.

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

     'Accessor' 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 in the vignette.

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

     Martin Morgan <mtmorgan@fhcrc.org>

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

     Vignette `Retrieving MAGE and ARR sample attributes'.

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

     ## defined and auto-generated classes
     names(slot(getClass("ARRCompatibility",
                         where=getNamespace("AffyCompatible")),
                "subclasses"))

