hgu133a.pdnn.params         package:affypdnn         R Documentation

_C_h_i_p-_t_y_p_e _s_p_e_c_i_f_i_c _d_a_t_a

_D_e_s_c_r_i_p_t_i_o_n:

     Chip-type specific data structure.

_U_s_a_g_e:

     data(hgu95av2.pdnn.params)

_F_o_r_m_a_t:

     The format is a list:

     _E_g environment (one entry per dinucleotide)

     _W_g numerical vector.

     _E_n environment (one entry per dinucleotide)

     _W_n numerical vector.

     _g_e_n_e._S_n list (one entry per affyID)

     _g_e_n_e._S_g list (one entry per affyID)

     _g_e_n_e._x_y list (one entry per affyID)

     _p_a_r_a_m_s._g_e_n_e environment

_D_e_t_a_i_l_s:

     These chip-specific data structures are generated from the data
     files made available by the author of the PDNN paper (see the
     section source). They are stored as 'data' to save some
     computation time. The data structures were made using the function
     'pdnn.params.chiptype'. The data files are included in the the
     directory `data' of the package.

_N_o_t_e:

     To lower the size of the package, the only chip-specific data
     structures included in the package is the one for HG-U95Av2.

_S_o_u_r_c_e:

     Li Zhang, Michael F. Miles and Kenneth D. Aldape - A model of
     molecular interactions on short oligonucleotide arrays, 2003,
     Nature Biotech., vol. 21, n.7

_E_x_a_m_p_l_e_s:

     ## give the path the original energy parameter files included in the package
     list.files(system.file("exampleData", package="affypdnn"),
                "^pdnn-energy-parameter_", full.names=TRUE)

