idProteinErrorType         package:ppiStats         R Documentation

_A _f_u_n_c_t_i_o_n _t_o _i_d_e_n_t_i_f_y _t_h_o_s_e _p_r_o_t_e_i_n_s _a_f_f_e_c_t_e_d _b_y _e_i_t_h_e_r
_s_t_o_c_h_a_s_t_i_c _o_r _s_y_s_t_e_m_a_t_i_c _e_r_r_o_r_s

_D_e_s_c_r_i_p_t_i_o_n:

     This function takes in either a bait to prey Graph (matrix) and,
     based on a binomial error model, partitions proteins identified as
     either affected by systematic or stochastic error.

_U_s_a_g_e:

     idSystematic(bpMat, viable, bpGraph = FALSE, pThresh = 0.01, pLevels = 1e-4, prob=0.5)
     idStochastic(bpMat, bpGraph = FALSE, pThresh = 0.01, pLevels = 1e-4, prob=0.5)

_A_r_g_u_m_e_n_t_s:

   bpMat: Either a bait to prey directed graphNEL or its corresponding
          adjacency matrix.

  viable: This is a character vector of viable proteins. It is only
          used in the idSystematic function.

 bpGraph: A logical. If TRUE, than bpMat is passed in by the user as a
          graphNEL.

 pThresh: The p-value threshold for which to partition stochastic or
          systematic errors

 pLevels: A numeric vector. It gives the levels to calculate the
          countours of the function in p in the (n-in, n-out)-plane

    prob: A numeric. The bias of the coin in the call to pbinom.

_V_a_l_u_e:

     A character vector of proteins either affected by systematic or
     stochastic errors.

_A_u_t_h_o_r(_s):

     T Chiang

_R_e_f_e_r_e_n_c_e_s:

     ~put references to the literature/web site here ~

_E_x_a_m_p_l_e_s:

     library(ppiData)
     idSystematic(Ito2001BPGraph, viableBaits[[1]], bpGraph=TRUE)

