mergeComplexes           package:apComplex           R Documentation

_I_t_e_r_a_t_i_v_e_l_y _c_o_m_b_i_n_e _c_o_l_u_m_n_s _i_n _i_n_i_t_i_a_l _P_C_M_G _e_s_t_i_m_a_t_e

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

     Repeatedly applies the function 'LCdelta' to make combinations of
     columns in the affiliation matrix representing the protein complex
     membership graph (PCMG) for AP-MS data.

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

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

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

    PCMG: Current PCMG estimate

  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:

     The Protein Complex Membership Graph (PCMG) algorithm for AP-MS
     data described by Scholtens and Gentleman (2004) uses a
     two-component measure of protein complex estimate quality, namely
     P=LxC.  Columns in 'cMat' represent individual complex estimates. 
     The PCMG algorithm works by starting with a maximal BH-complete
     subgraph estimate of 'cMat', and then improves the estimate by
     combining columns.  

     When proposing combinations of columns 'comp1' and 'comp2' in the
     PCMG estimate 'cMat', the proposal is accepted if the output from
     LCdelta (the log of LxC) is greater than zero.   'mergeComplexes'
     performs all column combinations until no more combinations result
     in an output from LCdelta greater than zero.

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

     An affiliation matrix representing the estimated PCMG.  The number
     of rows and row labels of the matrix will be the same as 'adjMat'.
      The number of columns will be less than or equal to the number of
     columns in 'adjMat'.

_W_a_r_n_i_n_g:

     ....

_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:

     'LCdelta','findComplexes'

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

     # to be added

