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(R) 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"))

