findComplexes           package:apComplex           R Documentation

_E_s_t_i_m_a_t_e _a _P_r_o_t_e_i_n _C_o_m_p_l_e_x _M_e_m_b_e_r_s_h_i_p _G_r_a_p_h (_P_C_M_G) _u_s_i_n_g _p_r_o_t_e_i_n _c_o_m_p_l_e_x _c_o_m_e_m_b_e_r_s_h_i_p _d_a_t_a _f_r_o_m _A_P-_M_S _t_e_c_h_n_o_l_o_g_y

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

     Performs all steps in the PCMG algorithm described by Scholtens
     and Gentleman (2004), beginning with an adjacency matrix recording
     bait-hit AP-MS data.

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

     findComplexes(adjMat, simMat = NULL, sensitivity = 0.75, specificity = 0.995, beta = 0)

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

  adjMat: Adjacency matrix of bait-hit data from an AP-MS experiment. 
          Rows correspond to baits and columns to hits.

  simMat: An optional square matrix with entries between 0 and 1.  Rows
          and columns correspond to the proteins in the experiment, and
          should be reported in the same order as the columns of
          dataMat.  Higher values in this matrix are interpreted to
          mean higher similarity for protein pairs.

sensitivity: Believed sensitivity of AP-MS technology.

specificity: Believed specificity of AP-MS technology.

    beta: Optional additional parameter for the weight to give data in
          'simMat' in the logistic regression model.

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

     'findComplexes' performs all steps in the PCMG algorithm using the
     apComplex package functions 'bhmaxSubgraph', 'LCdelta', and
     'mergeComplexes'.  These steps can also be performed separately by
     the user.

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

     An affiliation matrix representing the estimated PCMG.

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

     Denise Scholtens

_R_e_f_e_r_e_n_c_e_s:

     Scholtens, D. and Gentleman, R.  Making sense of high throughput
     protein-protein interaction data. (2004).

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

     'bhmaxSubgraph',code{LCdelta},'mergeComplexes'

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

     # to be added

