applyDeformationError     package:simulatorAPMS     R Documentation

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

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

     This function simulates False Negative (FN) observations on those
     bait proteins known to have been deformed during the AP-MS
     process.

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

     applyDeformationError(foundPrey, rateDeform)

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

foundPrey: A character vector of proteins names that interact with the
          a particular deformed protein P

rateDeform: The rate at which the deformation in P produces false
          negative observations within the AP-MS technology

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

     If there is a non-trivial number of deformed bait proteins, the
     function 'runSimulators' calls the intermediary function
     'simulatorD'. This latter function controls
     'applyDeformationError' by examining the arguments and parameters.
     For each deformed bait, 'simulatorD' calls this function to
     generate deformation errors.

     This is essentially a function for recording more FN interactions
     among baits and prey. The function takes in a bait that is known
     to have some deformation as a result of the experimentation.

     In essence, the bait loses some capacity to pull other proteins
     with which it would normally interact.

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

     The character vector, missedPrey:

     The return value missedPrey is a vector which is a subset of the
     vector foundPrey. This subset will be the proteins which will be
     included as FN observations due to the systematic errors via the
     deformation of protein P.

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

     T. Chiang

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

     'applyFNErrors, \code{runSimulators}'

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

     data(TSNMatrix)
     exampleFoundPrey <- rownames(TSNMatrix)[1:50]
     applyDeformationError(exampleFoundPrey, 0.5)

