sortComplexes           package:apComplex           R Documentation

_S_o_r_t _c_o_m_p_l_e_x _e_s_t_i_m_a_t_e_s

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

     Sorts complexes recorded in PCMG affiliation matrix into three
     separate affiliation matrices containing MBME, SBMH, and UnRBB
     complexes.

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

     sortComplexes(PCMG, adjMat)

_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.

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

     MBME complexes contain multiple bait proteins and multiple edges. 
     SBMH complexes contain one bait and a collection of hit-only
     proteins.  UnRBB complexes contain only two baits (no hit-only
     proteins) that are connected by an unreciprocated edge.

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

     A list of affiliation matrices representing the MBME, SBMH, and
     UnRBB complex estimates.

_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:

     'findComplexes'

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

     data(apEX)
     PCMG2 <- findComplexes(apEX,sensitivity=.7,specificity=.75)
     sortComplexes(PCMG2,apEX)

