idProteinType            package:ppiStats            R Documentation

_A _f_u_n_c_t_i_o_n _t_o _d_e_t_e_r_m_i_n_e _v_i_a_b_l_e _b_a_i_t_s, _v_i_a_b_l_e _p_r_e_y_s, _o_r
_h_o_m_o_d_i_m_e_r_s _w_i_t_h_i_n _e_x_p_e_r_i_m_e_n_t_a_l _d_a_t_a-_s_e_t_s.

_D_e_s_c_r_i_p_t_i_o_n:

     These functions take a bait to prey directed graphNEL and returns
     either a character vector of all proteins which participates in
     homodimer relationships or a list of three character vectors: a
     vector of viable baits, a vector of viable prey, and a vector of
     the viable bait/prey.

_U_s_a_g_e:

     idViableProteins(bpGraph, homomer=TRUE)
     idHomodimers(bpGraph)

_A_r_g_u_m_e_n_t_s:

 bpGraph: A directed graphNEL

 homomer: A logical. If True, homomer relationships will also be used
          to  characterize proteins as viable baits, viable prey, and
          also as viable bait/prey simultaneously. If False, those
          proteins whose only intraction is a homomer relationship will
          not be  characterized as viable in any context.

_V_a_l_u_e:

     The return value for idHomodimers is a character vector of those
     proteins which participates in homomer relationships.

     The return value for idViableProteins is a list of two character
     vectors:

      VB: A vector of baits that finds at least one prey in the
          experimental graphNEL, i.e. the nodes with out-degree at
          greater than 0. If homomer = FALSE, those proteins which
          participate in  only homomer relationships will not be
          returned.

      VP: A vector of prey which is found by at least one bait in the
          experimental graphNEL, i.e. the nodes with in-degree at
          greater than 0. If homomer = FALSE, those proteins which
          participate in  only homomer relationships will not be
          returned.

     VBP: A vector of proteins that are both viable baits and viable
          prey in an experimental dataset as defined above. If  homomer
          = FALSE, those proteins which participate in  only homomer
          relationships will not be returned.

_A_u_t_h_o_r(_s):

     T Chiang

_E_x_a_m_p_l_e_s:

     library(ppiData)
     idViableProteins(ItoCore2001BPGraph)
     idHomodimers(ItoCore2001BPGraph)

