degreeEstimates           package:ppiStats           R Documentation

_E_s_t_i_m_a_t_e _p_e_r-_n_o_d_e _d_e_g_r_e_e _i_n _v_i_a_b_l_e _b_a_i_t-_p_r_e_y (_V_B_P) _g_r_a_p_h _u_s_i_n_g _m_a_x_i_m_u_m
_l_i_k_e_l_i_h_o_o_d.

_D_e_s_c_r_i_p_t_i_o_n:

     Estimate per-node degree in viable bait-prey (VBP) graph using
     maximum likelihood.

_U_s_a_g_e:

     degreeEstimates(m,pTP,pFP)
     findDegree(rd,ud,pTP,pFP,N)
     degreePMF(deltahat,rd,ud,pTP,pFP,N)

_A_r_g_u_m_e_n_t_s:

       m: Square incidence matrix for VBP graph.

     pTP: True positive probability.

     pFP: False positive probability.

      rd: Observed number of reciprocated edges.

      ud: Observed number of unreciprocated edges.

deltahat: Estimate of node degree.

       N: Number of proteins which were tested twice (e.g. both as
          viable bait and as viable prey.)  Should equal the number of
          rows of m.

_D_e_t_a_i_l_s:

     'degreeEstimates' returns per-node degree estimates using the
     maximum likelihood method of Scholtens et al. (Submitted).  It
     takes arguments 'm', which is an incidence matrix of bait-prey
     relationships, typically a VBP graph filtered for proteins prone
     to systematic bias, as well as pTP and pFP values, globally
     applicable to the entire graph.

     'degreeEstimates' calls the function 'findDegree' which estimates
     degree for a single node, given its observed number of
     reciprocated and unreciprocated incident edges.  'findDegree'
     takes an argument 'N' which is the number of proteins in the graph
     that were tested twice.  When 'degreeEstimates' calls
     'findDegree', 'N' is set to the first dimension of the incidence
     matrix 'm'.  

     'degreePMF' calculates the value of the pmf for an estimated
     degree, given observed numbers of reciprocated and unreciprocated
     edges, as well as pTP, pFP, and N.  It is not generally called
     directly by the user.  It is used to locate the maximum likelihood
     estimator for degree.

_V_a_l_u_e:

     'degreeEstimates' returns a named vector of degree estimates for
     each node in the graph.

     'findDegree' returns a single degree estimate for one node.

     'degreePMF' returns the value of the pmf for the multinomial model
     at a specified estimate of node degree, given the number of
     observed reciprocated and unreciprocated edges incident on the
     node and pTP and pFP.

_A_u_t_h_o_r(_s):

     Denise Scholtens, dscholtens@northwestern.edu

_R_e_f_e_r_e_n_c_e_s:

     Scholtens D, Chiang T, Huber W, Gentleman R.  Estimating node
     degree in bait-prey graphs. (Submitted).

_E_x_a_m_p_l_e_s:

     findDegree(rd=2,ud=2,pTP=0.75,pFP=0.001,N=1000)

