runAPComplex          package:simulatorAPMS          R Documentation

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_o_n _t_h_e _s_i_m_u_l_a_t_e_d _o_u_t_p_u_t _f_r_o_m _r_u_n_S_i_m_u_l_a_t_o_r_s

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

     The runAPComplex function takes the simulated AP-MS experimental
     data (represented as an adjacency matrix) and deletes the proteins
     from this matrix that is either not used as a bait nor ever seen
     as a prey in the experiment. After the deletion, the apComplex is
     called on the resulting matrix.

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

     runAPComplex(errorModel, vBaits)

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

errorModel: An adjacency matrix: the rows are indexed by the baits and
          the columns are indexed by all the proteins found in the
          organism or cell under certain conditions

  vBaits: A character vector: baits used in the simulated AP-MS
          experiment

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

     This function runs the estimation algorithm apComplex. The
     algorithm accomplishes two things: it makes decision on if a
     directed edge is a True Positive (TP) or False Positive (FP) and
     if a missing directed edge is a True Negative (TN) or False
     Negative; after total reciprocity is decided, apComplex estimates
     the protein complex bi-partite graph matrix.

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

     The return value errorComplex is the Bi-partite Graph Incidence
     Matrix estimated by apComplex.

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

     Tony Chiang

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

     #data(TSNMatrix)
     #data(vBaits)
     #data(missedProtEX)
     #sim = runSimulators(TSNMatrix, vBaits, vBaits[2], vBaits[5], 0.0003,
     #0.1, 0, 0, missedProtEX, 357)
     #runAPComplex(sim, vBaits)

