inNucleus              package:y2hStat              R Documentation

_A _f_u_n_c_t_i_o_n _t_o _d_e_t_e_r_m_i_n_e _t_h_o_s_e _p_r_o_t_e_i_n_s _a_n_n_o_t_a_t_e_d _b_y _t_h_e _n_u_c_l_e_u_s
_G_O _t_e_r_m.

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

     This function takes the experimental y2h data as well as an
     estimate for an in silico interactome (ISI) and determines which
     protein complexes of the ISI has more than 75 percent of the
     constituent member proteins annotated by the nucleus GO term.

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

     inNucleus(y2h, ISI = NULL)

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

     y2h: A three tiered list. Names of the second tier corresponds to
          ID of experiment. Names of the third tier should be the bait
          proteins. The entries of the third tier are character vectors
          of proteins detected as prey

     ISI: The incidence matrix of the bi-partite graph representation
          of the in silico interactome.

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

 nucProt: A character vector of those proteins annotated to the nucleus

 nucComp: An incidence matrix of the bipartite graph representation of
          the ISI with the restriction that only complexes with 75
          percent of its constituent members are annnotated by the
          nucleus term.

nuclearY2H: A data structure exactly like the input y2h, except that
          the prey proteins are restricted to those which are annotated
          by the nucleus term

_A_u_t_h_o_r(_s):

     T Chiang

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

     data(y2hSysGW)
     eg=y2hSysGW[3]
     inNucleus(eg)

