calcICs                package:GOSim                R Documentation

_C_a_l_c_u_l_a_t_e _i_n_f_o_r_m_a_t_i_o_n _c_o_n_t_e_n_t_s _o_f _G_O _t_e_r_m_s.

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

     Recalculates the information content of all GO terms.

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

     calcICs()

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

     none

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

     This functions should only be invoked, if one wants to calculate
     the information content for GO terms with respect to combinations
     of evidence codes other than the precomputed ones or, if a  new
     version of the "GO" library has been installed. By default the
     information contents are precomputed using all evidence codes and
     evidence codes "IMP, IGI, IDA, IEP, IPI" together.

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

     Puts a file named "ICs<ontology><evidence levels>.rda" in the
     current directoy. This file has then to be moved into the data
     directory of gosim.

_S_e_e _A_l_s_o:

     'setEvidenceLevel'

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

                   
     ## Not run: 
       setOntology("CC")
       calcICs()
     ## End(Not run) # --> this may take some time ...

