equivSummary           package:goProfiles           R Documentation

_T_h_i_s _f_u_n_c_t_i_o_n _r_e_t_u_r_n_s _a _b_r_i_e_f _s_u_m_m_a_r_y _o_f _t_h_e _e_q_u_i_v_a_l_e_n_c_e _t_e_s_t _b_e_t_w_e_e_n _t_w_o _p_r_o_f_i_l_e_s.

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

     Function to return a brief summary of the equivalence test between
     two profiles. If In its current version it is better that
     'equivalentGOProfiles' is called with option 'simplify' set to
     'FALSE' before 'equivSummary' can be used

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

     equivSummary(l, decs = 6)

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

       l: A list of comparison results as returned by a call to
          \texttt{compareGenelists}

    decs: Number of decimal places to use in the output

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

     A data frame with the summarized results of each comparison. The
     values contained are: \texttt{Sqr.Eucl.Dist}: The squared
     euclidean distance,  \texttt{Standard Err}: The standard error
     estimate, \texttt{pValue} p value of the equivalence test, 
     \texttt{up conf.int}Upper value for the desired condfidence
     interval. \texttt{d0}Threshold value for equivalence test.
     \texttt{Equivalent?}Numerical value set to 1 if profiles can be
     considered equivalent and to zero if they cannot.

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

     Alex Sanchez

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

     data(sampleProfiles)
     comparedMF <-compareGOProfiles (pn=expandedWelsh01[['MF']], 
                               qm  = expandedSingh01[['MF']], 
                               pqn0= commonExpandedWelsh01Singh01[['MF']])
     equivMF<- equivalentGOProfiles(comparedMF)
     print(equivSummary(equivMF, decs=5))

