hyperGTest              package:GOstats              R Documentation

_H_y_p_e_r_g_e_o_m_e_t_r_i_c _T_e_s_t_s _f_o_r _G_O _t_e_r_m _a_s_s_o_c_i_a_t_i_o_n

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

     Given a 'GOHyperGParams' instance containing a set of unique
     Entrez Gene Identifiers, a microarray annotation data package
     name, and the GO ontology of interest, this function will compute
     Hypergeomtric p-values for over or under-representation of each GO
     term in the specified ontology among the GO annotations for the
     interesting genes.  The computations can be done conditionally
     based on the structure of the GO graph.

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

       p: A 'GOHyperGParams' instance 

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

     When 'conditional(p) == TRUE', the 'hyperGTest' function uses the
     structure of the GO graph to estimate for each term whether or not
     there is evidence beyond that which is provided by the term's
     children to call the term in question statistically
     overrepresented.

     The algorithm conditions on all child terms that are themselves
     significant at the specified p-value cutoff.  Given a subgraph of
     one of the three GO ontologies, the terms with no child categories
     are tested first.  Next the nodes whose children have already been
     tested are tested.  If any of a given node's children tested
     significant, the appropriate conditioning is performed.

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

     A 'GOHyperGResult' instance.

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

     Seth Falcon

_R_e_f_e_r_e_n_c_e_s:

     FIXME

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

     'GOHyperGResult-class' 'geneCategoryHyperGeoTest'
     'geneGoHyperGeoTest' 'geneKeggHyperGeoTest'

