clusterSignifBase-class      package:goCluster      R Documentation

_C_l_a_s_s "_c_l_u_s_t_e_r_S_i_g_n_i_f_B_a_s_e"

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

     This class provides a very simple selection mechanism to identify
     interesting annotation terms.

_D_e_t_a_i_l_s:

     The class provides a wrapper around the 'selectStats' function.
     Please read the corresponding documentation for further details.

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

     '_t_h_r_e_s_h_o_l_d': Object of class '"numeric"', the threshold for
          selecting interesting annotation terms. This threshold is
          applied to the statistic returned by the
          'clusterStatistic'-class and any terms with a p-value lower
          than the threshold will be returned.

     Additional slots are described in the documentation of the
     'clusterSignif-class' and 'clusterModule-class'.

_E_x_t_e_n_d_s:

     Class '"clusterSignif"', directly. Class '"clusterModule"', by
     class '"clusterSignif"'.

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

     _c_o_n_f_i_g 'signature(object = "clusterSignifBase")': interactive
          setup of the class. You can set the threshold here.

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

     _s_e_t_u_p<- 'signature(object = "clusterSignifBase")': non-interactive
          setup of the class. You need to provide a list that contains
          the necessary settings for the class. 

     _e_x_e_c_u_t_e 'signature(object = "clusterSignifBase")': selects
          annotation terms that have a p-value lower than the given
          threshold. 

     _r_e_s_e_t 'signature(object = "clusterSignifBase")': resets the
          results of this class so that the selection process can be
          run again. 

     _p_r_i_n_t 'signature(object = "clusterSignifBase")': This function
          prints some basic information about the content of this
          object. If the object has been executed, it will show the
          number of identified annotation terms. 

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

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

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

     'selectStats', 'goCluster-class', 'clusterSignif-class',
     'clusterModule-class'

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

     ## Load a small test dataset
     data(benomylsetupsmall)

     ## Create an emty goCluster object
     test <- new("goCluster")

     ## Modify the configuration to use this significance class
     benomylsetupsmall$classsign <- "clusterSignifBase"

     ## Assign the configuration to the object and directly execute it
     execute(test) <- benomylsetupsmall

     ## This should show you the selected annotations. They should
     ## all have a value below 0.05.
     test@sign@selection

