compBijection         package:simulatorAPMS         R Documentation

_F_u_n_c_t_i_o_n _t_h_a_t _c_a_l_c_u_l_a_t_e_s _a_n _a_l_i_g_n_m_e_n_t _b_e_t_w_e_e_n _I_S_I _a_n_d _e_s_t_i_m_a_t_e
_b_a_s_e_d _o_n _s_o_m_e _s_i_m_i_l_a_r_i_t_y _m_e_a_s_u_r_e, _e._g _J_a_c_c_a_r_d

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

     This function takes a similarity measure matrix between the ISI
     and some estimate and finds the maximal value of this matrix. It
     aligns the complex indexed by the row and the complex indexed by
     the column and deletes the row and colunm and recursively calls
     itself on the new matrix. It stops when there are either no rows
     left or no columns left. The function breaks ties by comparing
     complex size and taking the larger complexes.

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

     compBijection(TSNMat, estMat, c2kMatrix, bijMat, counter = 1)

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

  TSNMat: matrix for bipartite graph for ISI 

  estMat: matrix for bipartite graph of the estimate 

c2kMatrix: similarity matrix; e.g, Jaccard

  bijMat: matrix that will store the alignment and the similarity
          between the two complexes

 counter: keeps tracks of the number of complexes aligned

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

     This function tries to create a maximal alignment. It will use the
     minimum number of complexes (either the number of complexes in ISI
     or the estimate) as the number of complexes to align. This number
     varies from estimate to estimate, so the number of rows in bijMat
     must vary accordingly. Therefore, the runAlignment() function must
     be called first to set up BijMat.

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

     Matrix: where each row gives the alignment between ISI and
     estimate and the corresponding similarity index.

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

     Tony Chiang

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

     library(simulatorAPMS)
     data(simEX)
     data(APComEX)
     CC = runCompareComplex(simEX, APComEX)
     JC = JaccardCoef(CC)
     runAlignment(simEX, APComEX, JC)

