clusterData-class         package:goCluster         R Documentation

_C_l_a_s_s "_c_l_u_s_t_e_r_D_a_t_a", _a _c_l_a_s_s _f_o_r _h_o_l_d_i_n_g _d_a_t_a_s_e_t_s _t_h_a_t _a_r_e _g_o_i_n_g
_t_o _b_e _a_n_a_l_y_s_e_d _w_i_t_h _g_o_C_l_u_s_t_e_r.

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

     This class provides a container for microarray data.

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

     This class provides a wrapper for 'exprSet' objects from
     bioconductor. It provides a link to the annotation data in
     goCluster. A vector of unique ids that connects each element (row)
     in the dataset with its corresponding annotation terms has to be
     provided.

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

     '_n_a_m_e': Object of class '"character"', a name for the dataset.

     '_d_a_t_a_s_e_t': Object of class '"exprSet"', the dataset for the
          analysis.

     '_u_n_i_q_u_e_i_d': Object of class '"character"', the unique id for each
          gene (row) in the dataset.

     '_a_n_n_o': Object of class '"clusterAnnotation"', the annotation
          object that holds the annotation to this dataset.

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

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

     Class '"clusterModule"', directly.

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

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

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

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

     _e_x_e_c_u_t_e 'signature(object = "clusterData")': passes the
          'execute'-call to the annotation object. 

     _e_x_e_c_u_t_e<- 'signature(object = "clusterData")': passes the
          'execute<-'-call to the annotation object. 

     _r_e_s_e_t 'signature(object = "clusterData")': This only conveys the
          reset signal to the clusterAnnotation object. The dataset of
          the clusterData object will not be removed by this reset
          method. A new 'goCluster'-object should be created for each
          new dataset. 

     _p_r_i_n_t 'signature(object = "clusterData")': calls the print
          function of the exprSet-object stored in the dataset slot. 

_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:

     'goCluster-class', 'clusterAnnotation-class', 'setup', 'setup<-',
     'execute', 'reset'.

