collectIntactData          package:y2hStat          R Documentation

_A _f_u_n_c_t_i_o_n _t_h_a_t _p_a_r_s_e_s _t_h_e _I_n_t_a_c_t _r_e_p_o_s_i_t_o_r_y _f_o_r _b_a_i_t _t_o _p_r_e_y _a_f_f_i_l_i_a_t_i_o_n

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

     This function is the parsing function for the Intact downloaded
     data-sets.

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

     collectIntactData(intactID)

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

intactID: A character vector of the Intact ID's that reference the
          particular experiment needed to be parsed.

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

     The collectIntactData is a general function that reads a
     downloaded (and organized) xml file, and gathers information for
     the set of desired experiments.

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

numBaits: The number of distinct baits over all experiments

numPreys: The number of distinct preys over all experiments

allBaits: A character vector of all distince baits over all experiments

allPreys: A character vector of all distinct preys over all experiments

intactID: The intact ID's of all the experiments

indexSetAll: A list of lists. Each element of the top list corresponds
          to a particular experiment; the elements of these sub-lists
          are character vectors. The character vectors will always
          carry the bait protein in the first element and all of the
          preys that particular bait has found as the rest of the
          elements to the vector. Note that the multiplicity is not
          guarenteed to be unity.

baitsSystematic: A character vector with a number of baits mapped to
          their systematic names

preysSystematic: A character vector with a number of preys mapped to
          their systematic names

  shortL: A character vector listing the first author of each
          experiment.

tableList: The organized xml file parsed by the function.

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

     T Chiang

_R_e_f_e_r_e_n_c_e_s:

     http://www.ebi.ac.uk/intact

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

       inTactData <- collectIntactData(c("EBI-375746", "EBI-531419",
                                         "EBI-295760", "EBI-698096"))

