maigesRelNetB-class        package:maigesPack        R Documentation

_m_a_i_g_e_s_R_e_l_N_e_t_B _c_l_a_s_s, _s_t_o_r_e _r_e_s_u_l_t_s _o_f _r_e_l_e_v_a_n_c_e _n_e_t_w_o_r_k _a_n_a_l_y_s_i_s (_B_u_t_t_e'_s _m_e_t_h_o_d)

_D_e_s_c_r_i_p_t_i_o_n:

     This class defines a structure to store the results of relevance
     network analysis, using a method that was proposed by Butte et al.
     (2000), see the reference below. Objects of this type are
     generated calling the function 'relNetworkB'.

_D_e_t_a_i_l_s:

     Objects of this class are produced by calling the function
     'relNetworkB' over an object of class 'maiges' to search for pairs
     of genes with significant correlation values in a specific sample
     type, according to the method proposed by Butte et al. (2000).

_S_l_o_t_s:


     '_W': numeric matrix giving the W values of the genes tested. This
          information is useful for doing plots representing the
          correlation coefficient values.

     '_C_o_r_r': numerical square matrix that store the correlation
          coefficient values between all pair of genes tested.

     '_P_v_a_l': numerical square matrix that store the p-value for each
          correlation value between the pairs of genes.

     '_m_a_x_B': numerical square matrix that store the maximum (in
          absolute value) of the correlation values calculated by
          permutation values, as described by Butte et al. (2000).

     '_t_y_p_e_s': character vector giving the name of sample type tested.

     '_S_l_a_b_e_l': string with the sample label used to define the sample
          types tested.

     '_D_a_t_e': character string giving the date and time that the object
          was generated.

     '_V._i_n_f_o': list containg three characters. The first one is a
          string containing the R version used when the object was
          created. The second is a char vector with base packages and
          the last one is another char vector with additional packages
          and version numbers.

_M_e_t_h_o_d_s:


     _i_m_a_g_e 'signature(x = 'maigesRelNetB')': image method for
          'maigesRelNetB' class. Display colour representation of the
          correlation matrix.

     _p_l_o_t 'signature(x = 'maigesRelNetB')': plot method for
          'maigesRelNetB' class. Display a circular graph representing
          the relevance network.

     _p_r_i_n_t 'signature(x = 'maigesRelNetB')': print method for
          'maigesRelNetB' class.

     _s_h_o_w 'signature(x = 'maigesRelNetB')': show method for
          'maigesRelNetB' class.

     _s_u_m_m_a_r_y 'signature(x = 'maigesRelNetB')': summary method for
          'maigesRelNetB' class.

_A_u_t_h_o_r(_s):

     Gustavo H. Esteves <gesteves@vision.ime.usp.br>

_R_e_f_e_r_e_n_c_e_s:

     Butte, A.J.; Tamayo, P.; Slonim, D.; Golub, T.R. and Kohane, I.S.
     Discovering functional relationships between RNA expression and
     chemotherapeutic susceptibility using relevance networks. *PNAS*,
     97, 12182-12186, 2000. (<URL:
     http://www.pnas.org/cgi/content/full/97/22/12182>)

_S_e_e _A_l_s_o:

     'relNetworkB'.

