applyDeformationError     package:simulatorAPMS     R Documentation

_F_u_n_c_t_i_o_n _t_o _c_a_l_c_u_l_a_t_e _t_h_e _D_e_f_o_r_m_a_t_i_o_n _E_r_r_o_r_s _o_f _A_P-_M_S

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

     The applyDeformationError function simulates FN outputs for those
     proteins that might have been deformed during the baiting process.
     The parameters for the function implicitly define which protein,
     P, is deformed, since the foundPrey is the set of proteins in the
     ISI which all interact with P. The rateDeform is the rate at which
     the deformation causes P to accumulate FN's. The return value are
     those proteins which will become the deformation FN set for
     protein P in the simulated error model.

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

     applyDeformationError(foundPrey, rateDeform)

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

foundPrey: a vector of proteins that interact with protein P in the
          ISI; protein P is the protein that has been deformed.

rateDeform: a rate at which the deoformed protein P will record FN
          outputs in the experiment

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

     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 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 the FN's due to deformation of protein P.

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

     Tony Chiang

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

     'applyFNErrors, \code{runSimulators}'

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

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

       

