assessSymmetry           package:ppiStats           R Documentation

_A _f_u_n_c_t_i_o_n _t_h_a_t _c_a_l_c_u_a_l_t_e_s _s_o_m_e _d_i_r_e_c_t_e_d _d_e_g_r_e_e _s_t_a_t_i_s_t_i_c_s _o_n
_g_r_a_p_h_s _u_s_i_n_g _a _b_i_n_o_m_i_a_l _e_r_r_o_r _m_o_d_e_l

_D_e_s_c_r_i_p_t_i_o_n:

     This function takes in a bait to prey protein-protein interaction
     graph (undirected) and calculates the reciprocated degree, the
     unreciprocated in and out degrees. Using this information and
     binomial error model, it asses the p-value for the in and out
     degree of each protein. Lastly, it plots the countour curves for
     these p-values

_U_s_a_g_e:

     assessSymmetry(bpMat, bpGraph = FALSE,
       prob=0.5, pLevels = 1e-4)

_A_r_g_u_m_e_n_t_s:

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

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

 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 used in the function pbinom
          call.

_V_a_l_u_e:

     A list:

     deg: A 3xn matrix. The rows are indexed by each protein. Column
          one gives the number of reciprocated edges; column two gives
          the number of unreciprocated out edges; colunm three gives
          the number of unreciprocated in-edges

       p: The p-value for each protein with experimental in and out
          degrees

countours: The countours as a function of p

_A_u_t_h_o_r(_s):

     W Huber

_E_x_a_m_p_l_e_s:

     library(ppiData)
     assessSymmetry(Ito2001BPGraph, bpGraph=TRUE)

