mgeneSim               package:SemSim               R Documentation

_P_a_i_r_w_i_s_e _S_e_m_a_n_t_i_c _S_i_m_i_l_a_r_i_t_y _S_c_o_r_e_s _f_o_r _a _S_e_t _o_f _G_e_n_e _P_r_o_d_u_c_t_s

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

     Given a set of Entrez Gene IDs, this function returns pairwise
     semantic similarity or distance scores for all the gene products
     with GO annotations available.

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

     mgeneSim(genes, ont = "MF", measure = "Resnik", drop = "IEA", db = "UniProt", multiple = "max")

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

   genes: A set of Entrez Gene IDs.

     ont: One of "MF", "BP", and "CC" subontologies.

 measure: One of "Resnik", "Lin", "Rel", and "Jiang" methods.

    drop: A set of evidence codes based on which certain annotations
          are not considered. Use NULL to keep all GO annotations.

      db: Databases from which the information content has been
          derived. See description in 'termSim'.

multiple: See description in 'mtermSim'.

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

     A matrix of pairwise similarity scores for gene products with GO
     annotations available.

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

     'geneSim'

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

       data(Schreiber)
       sim<-mgeneSim(Schreiber, ont="BP", measure="Rel", multiple="rcmax")
       sim[1:3, 1:3]

