simulatorS           package:simulatorAPMS           R Documentation

_F_u_n_c_t_i_o_n _t_h_a_t _c_a_l_c_u_l_a_t_e_s _t_h_e _F_P _s_t_i_c_k_y _e_r_r_o_r_s

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

     The simulatorS function is the function that operates on sticky
     baits. It takes in a vector of sticky baits, and for each bait B,
     it finds all the proteins not interacting with it in the ISI. When
     it has calculated this set of proteins, it calls the
     applyStickyErrors function and gets the subset of proteins as the
     FP hits. It changes these interactions from 0 to 1 in the PPCM
     matrix creating an directed graph PPCM matrix with error.

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

     simulatorS(sticky, rateS, exMat)

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

  sticky: A vector of baits known to be sticky

   rateS: A single rate of a vector of rates which the experiment will
          record FP's due to the sticky proteins

   exMat: The experimental matrix that carries the FP/FN 

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

     One interesting aspect of this function is that the rateS can
     either be a vector of the same length as the vector of sticky
     baits, or it can be a single rate which is applied to all the
     sticky baits. The function calls applyStickyErrors on the
     prescribed sticky baits to assign FP observations onto them. This
     FP rate is different than the general rateFP and is determined by
     rateS

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

     The return value of this function is the adjusted PPCM matrix with
     error to reflect the FP's that have been induced by
     applyStickyErrors

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

     Tony Chiang

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

     'simulatorS'

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

     library(apComplex)
     data(MBMEcHMSPCI)
     data(HMSPCI)
     vBaits = rownames(HMSPCI)[1:10]
     PPI = MBMEcHMSPCI 
     mode(PPI) = "logical"
     mode(PPI) = "numeric"
     exMat = PPI[vBaits,]
     stickyBaits = vBaits[2:3]
     rateS = 0.9
     test = simulatorS(stickyBaits, rateS, MBMEcHMSPCI, exMat) 
     test[2:3,]

