compIndep           package:simulatorAPMS           R Documentation

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_b_e_t_w_e_e_n _t_w_o _b_i-_p_a_r_t_i_t_e _g_r_a_p_h _i_n_c_i_d_e_n_c_e _m_a_t_r_i_c_e_s.

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

     This function calculates the probability that a protein is in
     Cluster C-i and the probability that a protein is in cluster K-j
     and then the joint probability that the protein is in both C-i and
     K-j. The function compares the joint distributions with the
     marginals.

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

     compIndep(TSNMat, erMat, intersectMat)

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

  TSNMat: The first bi-partite graph matrix; usually a representation
          of the true state of nature.

   erMat: The second bi-partite graph mattrix; usually an estimate of
          the true state of nature based on some error model.

intersectMat: A matrix of of integers. The (i,j)th entry is the
          cardinality of the intersection between the i-th complex of
          TSNMat and the j-th complex of erMat.

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

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

     Matrix of real numbers:

     The return value is a matrix of real numbers that account for how
     independent the marginals are from the joint distribution of
     protein membership to complexes.

_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)
     compIndep(simEX, APComEX, CC[[1]])

