setEvidenceLevel            package:GOSim            R Documentation

_S_p_e_c_i_f_i_e_s _t_o _u_s_e _o_n_l_y _G_O _t_e_r_m_s _w_i_t_h _g_i_v_e_n _e_v_i_d_e_n_c_e _c_o_d_e_s.

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

     Specifies to use only GO terms with given evidence codes.

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

     setEvidenceLevel(evidences = "all")

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

evidences: character vector of evidence codes 

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

     Each evidence code can be one of: \begin{ldescription}

"_I_M_P" inferred from mutant phenotype

"_I_G_I" inferred from genetic interaction

"_I_P_I" inferred from physical interaction

"_I_S_S" inferred from sequence similarity

"_I_D_A" inferred from direct assay

"_I_E_P" inferred from expression pattern

"_I_E_A" inferred from electronic annotation

"_T_A_S" traceable author statement

"_N_A_S" non-traceable author statement

"_N_D" no biological data available

"_I_C" inferred by curator \end{ldescription}  Entrez Gene ids for which
     no GO associations exist are left out of the environment.

     Mappings were based on data provided by:

     Entrez Gene: <URL:
     http://gopher5/compbio/annotationSourceData/ftp.ncbi.nlm.nih.gov/gene/DATA/>.
     Built: Source data downloaded from Entrez Gene on Fri Sep 30
     02:51:32 2005

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

     none.

_N_o_t_e:

     The method directly uses the "GO" library to obtain the mappings
     of the Entrez Gene IDs to GO terms. Internally this mapping is
     especially used for calculating the information content of the GO
     terms. By default all evidence codes are used for this. If another
     behavior is wanted, one has to recalculate the information content
     of all GO terms via 'calcICs'. The evidence level also influences
     the behavior of 'filterGO' and 'getGOInfo'.

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

     Holger Froehlich

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

     <URL: http://www.ncbi.nih.gov/entrez/query.fcgi?db=gene>

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

     'calcICs', 'filterGO', 'getGOInfo'

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

             ## Not run: setEvidenceLevel("all") # the default behavior        

