applyFNErrors         package:simulatorAPMS         R Documentation

_F_u_n_c_t_i_o_n _t_o _c_a_l_c_u_l_a_t_e _F_N _E_r_r_o_r_s _i_n _A_P-_M_S

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

     The applyFNErrors is a function that simulates a random uniform FN
     outputs for all bait proteins used in the AP-MS experiementation.
     For each bait B, foundPrey is the set of proteins in the ISI that
     interacts with B. The parameter rateFN is the rate by which the
     AP-MS experiment records FN interactions. This FN rate is an
     estimate based on the stochastic nature of the technology.

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

     applyFNErrors(foundPrey, rateFN)

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

foundPrey: A vector of proteins that interacts with bait B in the TSN

  rateFN: The rate at which FN interactions are recorded in the AP-MS
          experiment

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

     During the AP-MS wet-lab experiments, a certain rate of proteins
     that are said to not interact are in fact false negative
     recordings. This function attempts to simulate the fact that this
     technology will fail to be consistent in the bait-prey pull down
     systems or fail to pull down true co-membership at all.

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

     The proteinsFN is a vector consisting of a subset of the foundPrey
     proteins which will serve as the FN output for bait B.

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

     Tony Chiang

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

     'applyFPErrors','applyDeformationError'

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

     library(simulatorAPMS)
     data(TSNMatrix)
     exampleFoundPrey <- rownames(TSNMatrix)[1:50]
     applyFNErrors(exampleFoundPrey, 0.3)
       

