runSimulators         package:simulatorAPMS         R Documentation

_F_u_n_c_t_i_o_n _t_h_a_t _s_e_t_s _u_p _t_h_e _I_S_I _e_t _a_l _t_o _r_u_n _t_h_e _s_i_m_u_l_a_t_i_o_n_s

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

     The runSimulators function is the primary function for the
     simulation tool. It first takes in an in the incidence matrix of
     the silico interactome's (ISI) bipartite graph representation.
     Since not all the proteins are documented in the ISI, it also
     appends all proteins found in the organism to the ISI. From there,
     we derive the Protein-Protein Co-Membership (PPCM) matrix. We then
     only take the rows indexed by baits, and apply all the simulated
     errors to this matrix. The result is an error model simulation of
     an AP-MS experiment.

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

     runSimulators(TSNMat, vBaits, vDeform, vStky, rateFP, rateFN, rateD, rateS, missedProt, seedIn)

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

  TSNMat: Incidence Matrix of ISI's bipartite graph representation

  vBaits: The vector of baits used in the simulated AP-MS experiment

 vDeform: The vector of deformed baits 

   vStky: The vector of sticky baits 

  rateFP: Rate at which AP-MS returns FP's 

  rateFN: Rate at which AP-MS returns FN's 

   rateD: Rate(s) at which the deformed baits return FN's 

   rateS: Rate(s) at which the sticky baits return FP's 

missedProt: The vector of proteins that have trivial co-membership and
          not recorded by the ISI

  seedIn: Seed used in the random generator which allows the user to
          set the seed for reproducible experiments

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

     The details of the function are as follows. TSNMat and vBaits have
     been described. The vStky and vDeformed are baits that account for
     systematic errors called sticky protein errors and deformed
     protein error, and the rateS and rateD are the rates for the
     respective systematic errors. The missedProt are those who are in
     no protein complex and thus not recorded in the ISI, but needed
     for simulation.

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

     The return value for this function is a rectangular matrix with
     rows indexed by the baits and the columns indexed by all proteins
     in the organism. This matrix will differ from the PPCM matrix in
     that it will have FN/FP's embedded from the simulated error
     functions.

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

     Tony Chiang

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

     'simulator'

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

     data(simEX)
     data(vBaits)
     data(missedProtEX)
     runSimulators(simEX, vBaits[2:4], vBaits[2], vBaits[3], 0.05, 0.1, 0, 0, missedProtEX, 357)

