bhmaxSubgraph           package:apComplex           R Documentation

_F_i_n_d _m_a_x_i_m_a_l _B_H-_c_o_m_p_l_e_t_e _s_u_b_g_r_a_p_h

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

     Given an adjacency matrix of bait-hit AP-MS protein data, this
     function finds the maximal BH-complete subgraphs and reports them
     as an affiliation matrix.

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

     bhmaxSubgraph(adjMat,VBs=NULL,VPs=NULL,unrecip=1)

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

  adjMat: 'adjMat' is an N by (N+M) adjacency matrix with N equal to
          the number of bait proteins and M equal to the number of
          hit-only proteins.  'adjMat' should have row and column names
          corresponding to the proteins in the experiment.  An entry of
          "1" in the ith row and jth column of 'adjMat' corresponds to
          bait protein i finding protein j as a hit.  All other entries
          should be 0. 

     VBs: 'VBs' is an optional vector of viable baits.

     VPs: 'VPs' is an optional vector of viable prey.

 unrecip: By default set to 1 so that unreciprocated bait-bait edges
          are treated as present.  If set to 0, unreciprocated
          bait-bait edges will be treated as absent.

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

     A BH-complete subgraph with n bait nodes and m hit-only nodes for
     AP-MS data is defined as a subgraph for which all n*(n-1)+nm
     directed edges exist.  A maximal BH-complete subgraph is a
     BH-complete subgraph which is not contained in any other
     BH-complete subgraph.

     If 'VBs' and/or 'VPs' are not specified, then by default 'VBs'
     will be assigned the set of baits that detect at least one prey
     and 'VPs' the set of prey that are detected by at least one bait.

     By default, unreciprocated bait-bait observations will be treated
     as present.  If 'unrecip' is set to 0, they will be treated as
     absent.  If the sensitivity of the AP-MS technology is believed to
     be less than the specificity, then it is suggested that
     'unrecip'=1.

     This function calls 'maxCliques' from the RBGL package.

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

     A list of length one named 'maxCliques' which is itself a list of 
     character vectors containing the names of the elements in the
     cliques.

_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:

     'mergeComplexes','findComplexes'

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

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

