simulator           package:simulatorAPMS           R Documentation

_F_u_n_c_t_i_o_n _s_e_t_s _u_p _i_n_p_u_t_s _t_o _c_a_l_l _a_l_l _F_N/_F_P _e_r_r_o_r_s _o_n _t_h_e _P_P_C_M

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

     For each bait, the simulator function first partitions all the
     proteins into two groups: (1) those that share co-membership with
     the bait in the ISI and (2) those that do not. From the first
     group, simulator calls the function applyFNErrors to generate the
     FN's for the error model; it calls applyFPErrors on the second
     group.

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

     simulator(TSNMat, exMat, bait, rateFP, rateFN)

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

  TSNMat: The PPCM matrix

   exMat: The error model matrix

    bait: A bait protein used in the simulated experiment 

  rateFP: The rate for which FP's are seen in the experiment 

  rateFN: The rate for which FN's are seen in the experiment 

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

     See description

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

     The return value is an directed graph matrix of PPCM with the
     embedded FN/FP's incorporated.

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

     Tony Chiang

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

     'runSimulators'

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

     data(simEX)
     data(vBaits)
     PPCM = simEX 
     mode(PPCM) = "logical"
     mode(PPCM) = "numeric"
     estMat = PPCM[vBaits[2:4],]
     rateFP = 0.025
     rateFN = 0.20
     simulator(simEX, estMat, vBaits[2], rateFP, rateFN)[2,]

