gtResult-class            package:PCpheno            R Documentation

_A _c_l_a_s_s _f_o_r _r_e_p_r_e_s_e_n_t_i_n_g _t_h_e _r_e_s_u_l_t _o_f _a _g_r_a_p_h_T_h_e_o_r_y _t_e_s_t.

_D_e_s_c_r_i_p_t_i_o_n:

     A class for representing the result of a 'graphTheory' test.

_S_l_o_t_s:


     '_P_v_a_l_u_e': Object of class '"numeric"'

     '_O_b_s_e_r_v_e_d': Return a '"numeric"' vector: the observed  number of
          interactions between genes inducing a specific phenotype and
          each cellular organizational units

     '_E_x_p_e_c_t_e_d': Return a matrix: the expected number of interactions
          between genes inducing a specific phenotype and each cellular
          organizational units

_E_x_t_e_n_d_s:

     Class '"testResult"', directly.

_M_e_t_h_o_d_s:


     '_p_l_o_t' Graphical representation of the test result

_A_u_t_h_o_r(_s):

     N. LeMeur

_S_e_e _A_l_s_o:

     'testResult','deResult','plot'

_E_x_a_m_p_l_e_s:

     ## apply a densityEstimate test 
     data(DudleyPhenoM)
     data(ScISIC)

     DudleyPhenoL <- apply(DudleyPhenoM,2,function(x) names(which(x==1)))
     NaCl <- DudleyPhenoL[["NaCl"]]

     perm <- 20 
     NaClGraph <- graphTheory(genename=NaCl, interactome=ScISIC,
     perm=perm)
      

     ## access results
     slotNames(NaClGraph)
     NaClGraph@Pvalue[1:5]

     ## use of the plot method
     plot(NaClGraph)

