createBPList             package:y2hStat             R Documentation

_A _f_u_n_c_t_i_o_n _t_o _c_r_e_a_t_e _t_h_e _B_a_i_t _t_o _P_r_e_y _a_s_s_o_c_i_a_t_i_o_n _l_i_s_t.

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

     This function takes the indexSetAll, baitsSystematic, and
     preysSystematic entries respectively from the output list of the R
     function collectIntactData, and it generates a three tier-ed list
     which ultimately records the bait to prey association from each
     yeast 2-hybrid experiment obtained from the IntAct repository.

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

     createBPList(indexSet, baitsSystematic, preysSystematic)

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

indexSet: A list of named lists. The names correspond to each
          experiment while the entries to the lower level lists are
          character vectors with two elements: the first element is the
          id for the bait protein and the second an id for the prey.
          This is an entry of the output of the collectIntactData
          function called indexSetAll

baitsSystematic: A named list. The names correspond to the IntAct
          acension codes for any proteins used as baits, and the
          entries of the list are character vectors consisting of
          Systematic gene names with respect to the IntAct ID. This is
          also an entry from the output of the function
          collectIntactData.

preysSystematic: A named list. The names correspond to the IntAct
          acension codes for any proteins used as preys, and the
          entries of the list are character vectors consisting of
          Systematic gene names with respect to the IntAct ID. This is
          also an entry from the output of the function
          collectIntactData.

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

     This function generates a three tiered list. The top tier is the
     main list. The second tier-ed set of lists should be named or
     referenced by experimentors. The third tier is a list of bait to
     prey associations. The names in the third tier of the list are
     those proteins sampled as baits, and the entries are character
     vectors of proteins detected as prey. This function will restrict
     those prey proteins to those which have also been sampled as
     baits. The resulting character vector contains only prey also
     sampled as baits or as a character(0)

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

     T Chiang

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

     data(y2h)
     eg = y2h$indexSetAll[3]
     eg1 = y2h$baitsSystematic[3]
     eg2 = y2h$preysSystematic[3]
     createBPList(eg, eg1, eg2)

