setOntology              package:GOSim              R Documentation

_S_e_t _a_n _o_n_t_o_l_o_g_y _a_s _b_a_s_e _f_o_r _s_u_b_s_e_q_u_e_n_t _c_o_m_p_u_t_a_t_i_o_n_s.

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

     Sets the ontology that all subsequent computations are based on
     and loads the information content of all GO terms within this
     ontology. At load time of the library the default ontology is
     "BP". Furtherm, on running this function the environment GOSimEnv
     is reinitialized, i.e. all global settings or parameters used in
     the library are reset to their default values.

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

     setOntology(ont = "BP")

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

     ont: the ontology to use ("BP","MF","CC") 

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

     The following ontologies can be used: \begin{ldescription}

"_B_P" biological process

"_M_F" molecular function

"_C_C" cellular component \end{ldescription}

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

     none.

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

     Holger Froehlich

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

      # set ontology to "molecular function"
     ## Not run: 
      setOntology("MF")
      # calculate Resnik similarity of two GO terms within this ontology
      getTermSim(c("GO:0004060","GO:0003867"),method="Resnik")
     ## End(Not run)

