genBPGraph              package:y2hStat              R Documentation

_A _f_u_n_c_t_i_o_n _t_o _g_e_n_e_r_a_t_e _t_h_e _Y_2_H _i_n_d_u_c_e_d _a_d_j_c_e_n_c_y _m_a_t_r_i_x _o_r _i_t_s
_c_o_r_r_e_s_p_o_n_d_i_n_g _g_r_a_p_h

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

     This function will take the Y2H data and generate either an
     adjacency matrix or an instance of the class graph.

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

     genBPGraph(y2h, sym = FALSE, inNuc = FALSE, nonWeighted = FALSE, homodimer = TRUE)

_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

     sym: A logical - if TRUE, only symmetric interactions will be used
          to generate the adjcency matrix or graph

   inNuc: A logical - if TRUE, only those proteins annotated to the
          nucleus GO terms will be used.

nonWeighted: A logical - if TRUE, the matrix will not determine the
          multiplicity of the interactions, but only the binary present
          or absent

homodimer: A logical - if FALSE, the matrix will not include the
          presence of homodimer interactions

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

     A list of adjaceny matrices based on the Y2H experimental data.

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

     T Chiang

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

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

