maigesActMod-class        package:maigesPack        R Documentation

_m_a_i_g_e_s_A_c_t_M_o_d _c_l_a_s_s, _s_t_o_r_e _r_e_s_u_l_t_s _o_f _f_u_n_c_t_i_o_n_a_l _c_l_a_s_s_i_f_i_c_a_t_i_o_n _o_f _g_e_n_e
_g_r_o_u_p_s

_D_e_s_c_r_i_p_t_i_o_n:

     This class defines a structure to store the results of functional
     classification of gene groups (or modules) that was proposed by
     Segal et al. (2004), see the reference below. Objects of this type
     are generated by calling the function 'activeMod'.

_D_e_t_a_i_l_s:

     Objects of this class are produced by calling the function
     'activeMod' over an object of class 'maiges' to search for gene
     groups that present numbers of genes induced or repressed greater
     than the expected by chance in biological sample types of
     interest. This is done according to the model proposed by Segal et
     al. (2004), described below.

_S_l_o_t_s:


     '_m_o_d_B_y_S_a_m_p': numerical matrix containing the fraction of genes
          activated (or negative fraction of genes repressed) for all
          chips. The rows and columns of the matrix represents the
          chips and the gene groups used, respectively.

     '_m_o_d_B_y_C_o_n_d': numerical matrix storing the fraction (or negative
          fraction) of different sample types that presents alteration
          in the gene groups tested. The rows and columns represents
          the sample types and gene groups, respectively.

     '_g_l_o_b_a_l_S_c_o_r_e': list with the same length as the number of gene
          groups containing matrices with the genes as rows and 2
          columns. The first column gives a global score that measure
          the consistency of the classification of the gene and the
          group, the second column gives the p-value for this score, as
          described in Segal et al. (2004).

     '_t_i_s_s_u_e_S_c_o_r_e': a list similar to the previous one, but having
          arrays of 3 dimensions that gives scores similar to that one
          described above, but relating only to each specific sample
          type. Note that this new score was implemented in this
          package and not in the original Segal's work.

     '_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 = 'maigesActMod')': image method for
          'maigesActMod' class. Display colour representation of the
          fractions of gene groups induced and repressed.

     _p_l_o_t 'signature(x = 'maigesActMod')': plot method for
          'maigesActMod' class. Do the same as image.

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

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

     _s_u_m_m_a_r_y 'signature(x = 'maigesActMod')': summary method for
          'maigesActMod' 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:

     Segal, E.; Friedman, N.; Koller, D. and Regev, A. A module map
     showing conditional activity of expression modules in cancer.
     *Nature Genetics*, 36, 1090-1098, 2004. (<URL:
     http://www.nature.com/ng/journal/v36/n10/abs/ng1434.html>)

_S_e_e _A_l_s_o:

     'activeMod'.

