applyFPErrors         package:simulatorAPMS         R Documentation

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

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

     The applyFPErrors is a function that simulates a random uniform FP
     outputs for all bait proteins used in the AP-MS experiementation.
     For each bait B, notFoundProt is the set of proteins in the ISI
     that does not have co-membership with B. The parameter rateFP is
     the rate by which the AP-MS experiment records FP interactions.
     The rateFP is estimated by the technologies stochastic nature.

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

     applyFPErrors(notFoundProt, rateFP)

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

notFoundProt: A vector of proteins that does not share any
          co-membership with bait B in the ISI

  rateFP: The rate at which FP interactions are recorded in the AP-MS
          experimentation

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

     During the AP-MS wet-lab experiments, a certain rate of proteins
     that are said to not have co-membership are in fact false postive
     recordings. This function attempts to simulate the fact that this
     technology will record interactions that are not present in the
     ISI.

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

     The proteinsFP is a vector consisting of a subset of the
     notFoundProt proteins which will serve as the FP output for bait B

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

     Tony Chiang

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

     'applyFNErrors', 'applyStickyError'

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

     library(simulatorAPMS)
     data(TSNMatrix)
     exampleNotFoundPrey <- rownames(TSNMatrix)[50:100]
     applyFPErrors(exampleNotFoundPrey, 0.04)
       

