simulatorD           package:simulatorAPMS           R Documentation

_F_u_n_c_t_i_o_n _t_h_a_t _s_i_m_u_l_a_t_e_s _d_e_f_o_r_m_a_t_i_o_n _e_r_r_o_r_s

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

     The simulatorD function is the function that operates on deformed
     baits. It takes in a vector of deformed baits, and for each bait
     B, it finds all the proteins interacting with it in the ISI. When
     it has calculated this set of proteins, it calls the
     applyDeformationErrors function and gets the subset of proteins as
     the FN hits. It changes these interactions from 1 to 0 in the PPCM
     matrix creating the error model.

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

     simulatorD(deformedBaits, rateD, TSNMat, exMat)

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

deformedBaits: Vector of deformed baits

   rateD: Either a single rate or a vector of rates which the
          experiment will record FN's 

  TSNMat: The PPCM matrix 

   exMat: The experimental matrix that carries the FN/FP 

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

     One interesting aspect of this function is that the rateD can
     either be a vector of the same length as the vector of deformed
     baits, or it can be a single rate which is applied to all the
     deformed baits. The function uses each rate to decide how deformed
     the bait has become and will create FN observations based on this
     data.

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

     The return value of this function is an PPCM matrix with error to
     reflect the FN's that have been induced by applyDeformationErrors

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

     Tony Chiang

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

     'applyDeformationError'

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

     data(MBMEcHMSPCI)
     data(HMSPCI)
     vBaits = rownames(MBMEcHMSPCI)[1:10]
     PPI = MBMEcHMSPCI 
     mode(PPI) = "logical"
     mode(PPI) = "numeric"
     exMat = PPI[vBaits[2:4],]
     deformedBaits = vBaits[3]
     rateD = 0.9
     test = simulatorD(deformedBaits, rateD, MBMEcHMSPCI, exMat) 
     test[3,]

