bpMatrix               package:y2hStat               R Documentation

_T_h_i_s _f_u_n_c_t_i_o_n _g_e_n_e_r_a_t_e_s _t_h_e _B_a_i_t-_P_r_e_y _M_a_t_r_i_x _f_o_r _a_n _e_x_p_e_r_i_m_e_n_t

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

     This function takes in experimental data and generates the bait to
     prey adjacency matrix.

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

     bpMatrix(y2h, symMat = TRUE, 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

  symMat: A logical, if TRUE, the matrix will be square with all the
          proteins documented in the experiment indexing both the row
          and column; if FALSE, only the baits index the rows, preys
          the columns.

homodimer: A logical. If true, the matrix will record the presence of
          homodimers; if FALSE, all homodimers data will be deleted.

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

     It is important to note that the weight of each directed edge is
     recorded by the number of instances bait b finds prey p.

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

     An adjacency matrix with weighting. The rows are indexed by those
     proteins sampled as baits (if symMat is true, only those rows with
     non-trivial row sums were sampled as baits) and the colunms are
     indexed by proteins detected as baits (et cetera).

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

     T Chiang

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

     data(y2hSysGW)
     eg <- y2hSysGW[3]
     bpMatrix(eg)

