clusterAlgorithmKmeans-class    package:goCluster    R Documentation

_C_l_a_s_s "_c_l_u_s_t_e_r_A_l_g_o_r_i_t_h_m_K_m_e_a_n_s", _p_r_o_v_i_d_e_s _k_m_e_a_n_s _c_l_u_s_t_e_r_i_n_g _f_o_r _g_o_C_l_u_s_t_e_r.

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

     This can be used to group a dataset according to kmeans. The
     resulting gene groups can subsequently be analysed for significant
     enrichment of specific annotations.

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

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

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

     '_r_e_p_e_a_t_s': Object of class '"numeric"', specifies how often the
          clustering should be repeated to account for the statistical
          variability of the clustering.

     '_c_l_u_s_t_e_r_s': Object of class '"numeric"', determines the number of
          clusters the kmeans clustering will identify.

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

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

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

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

     _c_o_n_f_i_g 'signature(object = "clusterAlgorithmKmeans")': interactive
          setup of the class. You will be asked to specify the number
          of clusters the kmeans clustering should result in and how
          often the clustering should be repeated.

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

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

     _e_x_e_c_u_t_e 'signature(object = "clusterAlgorithmKmeans")': run the
          clustering. 

     _r_e_s_e_t 'signature(object = "clusterAlgorithmKmeans")': remove all
          cluster data so that the 'execute' function can be run again.

     _p_r_i_n_t 'signature(object = "clusterAlgorithmKmeans")': This
          function prints some basic information about the content of
          this object.

_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:

     'clusterkmeans', 'goCluster-class', 'clusterModule-class',
     'clusterAlgorithm-class', 'clusterAlgorithmKmeans-class',
     'clusterAlgorithmClara-class', 'clusterAlgorithmPam-class'

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

     ## Predefined setup for goCluster
     data(benomylsetup)

     ## Change the setup to
     ## hierarchical clustering
     benomylsetup$classalgo <- "clusterAlgorithmKmeans"
     benomylsetup$algo$repeats   <- 10

     ## Setup a new goCluster object
     test <- new("goCluster")
     setup(test) <- benomylsetup

     ## Retrieve annotation
     test@data <- execute(test@data, test)

     ## Cluster the dataset
     test@algo <- execute(test@algo, test)

