runAPComplex          package:simulatorAPMS          R Documentation

~~_f_u_n_c_t_i_o_n _t_o _d_o ... ~~

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

     The runAPComplex function takes the simulated AP-MS experiment and
     deletes the proteins from the PPI 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 new PPCM matrix.

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

     runAPComplex(errorModel, vBaits)

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

errorModel: The simulated PPCM matrix where 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: The vector of 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 TP or FP and if a missing directed edge is a TN
     or FN; after total reciprocity is decided, apComplex estimates the
     protein complex interactome.

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

     The return value errorComplex is the Bipartite Graph Matrix
     estimated by apComplex

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

     Tony Chiang

