evalClusterHyper          package:goCluster          R Documentation

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_a_n_n_o_t_a_t_i_o_n _t_e_r_m_s _i_n _s_p_e_c_i_f_i_c _c_l_u_s_t_e_r_s.

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

     The function 'evalClusterHyper' moves through a tree of gene
     groups and  calls the function 'evalAnnosetHyper' for each of
     them. This second function employs the hypergeometric distributon
     to calculate a p-value for each of the annotation terms that is
     annotated to the genes in the group.

_U_s_a_g_e:

     evalClusterHyper(X, uniqueid, Annoset)
     evalAnnosetHyper(Selection, uniqueid, Annoset)

_A_r_g_u_m_e_n_t_s:

       X: The tree (list of lists) of clusters.

 Annoset: This is a list with each element holding a different
          annotation dataset. Each of this dataset is composed of two
          columns with the first column matching the ids of the genes
          given in the clusters, while the second column holds the
          corresponding annotation terms.

uniqueid: The unique id of the elements in the dataset. 

Selection: A list of genes that comprise one cluster. The ids given
          here have to match the ids from the first column of the
          annotation dataterms. 

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

     This class uses a "tree" (list of lists) of gene groups and
     analyzes the frequency of associated annotation terms within these
     groups using the hypergeometric distribution. For each group the
     unique annotation terms will be extracted and all genes matching
     these terms are selected as a reference set. The algorithm will
     then use the hypergeometric distribution to determine for each
     available annotation term in that group whether the genes in the
     group that match this term are enriched in this

_V_a_l_u_e:

 pvalues: Description of 'comp1'

selectedPerAnnotation: A vector that holds the number of times the
          annotation was found in the given selection. 

elementsPerAnnotation: A vector that holds the number of times the
          annotation was found over all elements.

selectedTotal: Total number of annotation terms in the given selection.

elementsTotal: Total number of annotation terms over all elements.

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

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

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

     'clusterStatisticHyper-class'

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

     ## FIXME

