coerce-method           package:maigesPack           R Documentation

_C_o_e_r_c_e _a _m_a_i_g_e_s _o_b_j_e_c_t _t_o _c_l_a_s_s_e_s _d_e_f_i_n_e_d _b_y _p_a_c_k_a_g_e_s _l_i_m_m_a _a_n_d _m_a_r_r_a_y

_D_e_s_c_r_i_p_t_i_o_n:

     Coercing methods were defined to convert maiges objects of classes
     'maiges' and 'maigesRaw' into objects of classes 'marrayNorm' and
     'marrayRaw' from package _marray_ or classes 'MAList' and 'RGList'
     from package _limma_ and vice-versa.

_U_s_a_g_e:

     ## S4 method for signature 'maiges, marrayNorm':
     as(from, to)

     ## S4 method for signature 'marrayNorm, maiges':
     as(from, to)

     ## S4 method for signature 'maiges, MAList':
     as(from, to)

     ## S4 method for signature 'MAList, maiges':
     as(from, to)

     ## S4 method for signature 'maigesRaw, marrayRaw':
     as(from, to)

     ## S4 method for signature 'marrayRaw, maigesRaw':
     as(from, to)

     ## S4 method for signature 'maigesRaw, RGList':
     as(from, to)

     ## S4 method for signature 'RGList, maigesRaw':
     as(from, to)

_A_r_g_u_m_e_n_t_s:

    from: object of class 'maiges', 'maigesRaw', 'MAList', 'RGList',
          'marrayNorm' or 'marrayRaw'.

      to: character string specifying the class of object to which the
          object 'from' will be coerced

_D_e_t_a_i_l_s:

     When converting from objects of classes 'RGList' or 'marrayRaw' to
     class 'maigesRaw', the slot 'Sf' and 'Sb' will always receive the
     channel 2 (red) values, and 'Rf' and 'Rb' will always receive
     channel 1 (green) values. For the normalized ojects, the slot 'W'
     will be equivalent to the M values.

     When converting from objects of classes 'maigesRaw' or 'maiges' to
     classes 'RGList', 'marrayRaw', 'MAList' or 'marrayNorm' the
     correct values of the two channels or of M values are calculated.

_M_e_t_h_o_d_s:


     _f_r_o_m = _m_a_i_g_e_s, _t_o = _m_a_r_r_a_y_N_o_r_m convert an object of class 'maiges'
          into an object of class 'marrayNorm'. 

     _f_r_o_m = _m_a_r_r_a_y_N_o_r_m, _t_o = _m_a_i_g_e_s convert an object of class
          'marrayNorm' into an object of class 'maiges'. 

     _f_r_o_m = _m_a_i_g_e_s, _t_o = _M_A_L_i_s_t convert an object of class 'maiges'
          into an object of class 'MAList'. 

     _f_r_o_m = _M_A_L_i_s_t, _t_o = _m_a_i_g_e_s convert an object of class 'MAList'
          into an object of class 'maiges'. 

     _f_r_o_m = _m_a_i_g_e_s_R_a_w, _t_o = _m_a_r_r_a_y_R_a_w convert an object of class
          'maigesRaw' into an object of class 'marrayRaw'. 

     _f_r_o_m = _m_a_r_r_a_y_R_a_w, _t_o = _m_a_i_g_e_s_R_a_w convert an object of class
          'marrayRaw' into an object of class 'maigesRaw'. 

     _f_r_o_m = _m_a_i_g_e_s_R_a_w, _t_o = _R_G_L_i_s_t convert an object of class
          'maigesRaw' into an object of class 'RGList'. 

     _f_r_o_m = _R_G_L_i_s_t, _t_o = _m_a_i_g_e_s_R_a_w convert an object of class 'RGList'
          into an object of class 'maigesRaw'. 

_N_o_t_e:

     It is possible to use Package _convert_ to convert objects between
     classes defined in packages _limma_, _marray_ and _Biobase_.

_S_e_e _A_l_s_o:

     'as' in the _methods_ package.

_E_x_a_m_p_l_e_s:

     ## Loading the dataset
     data(gastro)

     ## Converting a maigesRaw class object into marrayRaw object
     as(gastro.raw, "marrayRaw")

     ## Converting a maigesRaw class object into RGList
     as(gastro.raw, "RGList")

     ## Converting a maiges class object into marrayNorm object
     as(gastro.norm, "marrayNorm")

     ## Converting a maiges class object into MAList object
     as(gastro.summ, "MAList")

