compareComplex         package:simulatorAPMS         R Documentation

_F_u_n_c_t_i_o_n _t_o _c_o_m_p_a_r_e _t_h_e _I_S_I _t_o _t_h_e _e_s_t_i_m_a_t_e

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

     The compareComplex function takes two bipartite graph matrix
     representations and calculates three statistics between all pairs
     of complexes, C-i and K-j: (1) the protein intersection set, (2)
     the proteins in C-i and not in K-j, (3) the proteins in K-j and
     not in C-i. These stats are later used to calculate Jaccard and
     Dice-Sorenson Coefficients as well as probability distributions of
     a protein p in a complex C.

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

     compareComplex(TSNMat, erMat)

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

  TSNMat: ISI Bipartite Graph Matrix

   erMat: The Estimate Bipartite Graph Matrix

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

     The main point to remember is that we don't compare complexes
     within the same matrix. We only compare pairs of complexes from
     the ISI and its estimate. The runCompareComplex() function must be
     called first since all the proteins present in the ISI must be
     present in the estimate and vice versa so a true comparison can be
     made.

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

   comp1: A matrix of pairwise intersections between C-i and K-j. Rows
          are indexed by C-i and columns by K-j

   comp2: A matrix of pairwise set differences, C-i  K-j. Rows indexed
          by C-i and columns by K-j

   comp3: A matrix of pairwise set differences, K-j  C-i. Rows  indexed
          by C-i and columns by K-j

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

     Tony Chiang

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

     'runCompareComplex'

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

     library(apComplex)
     data(MBMEcHMSPCI)
     data(MBMEcTAP)
     runCompareComplex(MBMEcHMSPCI[,1:10], MBMEcTAP[,1:10])

