goCluster-class          package:goCluster          R Documentation

_C_l_a_s_s "_g_o_C_l_u_s_t_e_r", _a _c_l_a_s_s _f_o_r _c_o_m_b_i_n_i_n_g _c_l_u_s_t_e_r_i_n_g _r_e_s_u_l_t_s _w_i_t_h
_f_u_n_c_t_i_o_n_a_l _a_n_n_o_t_a_t_i_o_n

_D_e_s_c_r_i_p_t_i_o_n:

     This class provides a skeleton for the linkage of clustering
     results with statistical analysis of functional annotation.

_O_b_j_e_c_t_s _f_r_o_m _t_h_e _C_l_a_s_s:

     Objects can be created by calls of the form 'new("goCluster")'.

_S_l_o_t_s:

     '_d_a_t_a': Object of class '"clusterData"', the dataset that is going
          to be clustered.

     '_a_l_g_o': Object of class '"clusterAlgorithm"', the algorithm that
          is used for clustering.

     '_s_i_g_n': Object of class '"clusterSignif"', the function to
          estimate the significance of clusters based on the analysis
          of the associated annotation data.

     '_v_i_s_u': Object of class '"clusterVisual"', which provides methods
          to visualize of the results.

_M_e_t_h_o_d_s:

     _c_o_n_f_i_g 'signature(object = "goCluster")': interactive setup of the
          class. 

     _s_e_t_u_p 'signature(object = "goCluster")': returns the configuration
          as a list. This list can again be used for the
          non-interactive setup of the class. 

     _s_e_t_u_p<- 'signature(object = "goCluster")': non-interactive setup
          of the class. The option are specified using a list. 

     _r_u_n 'signature(object = "goCluster")': run goCluster as specified
          during setup. 

     _r_u_n<- 'signature(object = "goCluster")': run goCluster with the
          setting given as value to the assignment. 

     _r_e_s_e_t 'signature(object = "goCluster")': reset all results that
          were obtained during the last run of goCluster. 

     _d_i_s_p_l_a_y 'signature(object = "goCluster")': calls the display
          function of the clusterVisual object defined for the
          goCluster anaylsis. 

     _p_r_i_n_t 'signature(object = "goCluster")': calls the print function
          on each of the defined sub-objects. The output is being
          concatenated and returned to the user.

_A_u_t_h_o_r(_s):

     Gunnar Wrobel, <URL: http://www.gunnarwrobel.de>.

_S_e_e _A_l_s_o:

     'clusterAnnotation-class', 'clusterData-class',
     'clusterAlgorithm-class', 'clusterStatistic-class',
     'clusterSignif-class', 'clusterVisual-class', 'config', 'setup',
     'setup<-', 'execute', 'execute<-', 'reset' .

_E_x_a_m_p_l_e_s:

     ## Load the configuration and create a new
     ## goCluster object
     data(benomylsetup)
     test <- new("goCluster")

     ## Perform the analysis by using the execute<- method
     execute(test) <- benomylsetup

