LCdelta              package:apComplex              R Documentation

_C_o_m_p_u_t_e_s _c_h_a_n_g_e _i_n _L_x_C _m_e_a_s_u_r_e

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

     Computes the change in the P=LxC measure for AP-MS protein data
     when two protein complex estimates are combined into one complex.

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

     LCdelta(comp1, comp2, cMat, dataMat, baitList, simMat, mu, alpha, Beta, wsVal = 2e+07)

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

   comp1: Column index in 'cMat'.

   comp2: Column index in 'cMat'.

    cMat: Current protein complex membership estimate affiliation
          matrix.

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

baitList: A vector of the names of the proteins used as baits.

  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.

      mu: Parameter specification equal to
          log((1-specificitiy)/specificity).

   alpha: Parameter specification equal to
          log(sensitivity/(1-sensitivity)).

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

   wsVal: Workspace value to be used for computing Fisher's exact test.

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

     The local modeling algorithm for AP-MS data described by Scholtens
     and Gentleman (2004) and Scholtens, Vidal, and Gentleman
     (submitted) uses a two-component measure of protein complex
     estimate quality, namely P=LxC.  Columns in 'cMat' represent
     individual complex estimates.  The 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 is greater than zero.

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

     The numeric value of the change in P=LxC when columns 'comp1' and
     'comp2' in 'cMat' are combined into one column.

_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.  Statistical Applications in
     Genetics and Molecular Biology 3, Article 39 (2004).

     Scholtens D, Vidal M, and Gentleman R.  Local modeling of global
     interactome networks.  Bioinformatics 21, 3548-3557 (2005).

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

     'bhmaxSubgraph','mergeComplexes','findComplexes'

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

     data(apEX)
     PCMG0 <- bhmaxSubgraph(apEX)
     PCMG1 <- mergeComplexes(PCMG0,apEX,sensitivity=.7,specificity=.75)

