geneSim                package:SemSim                R Documentation

_S_e_m_a_n_t_i_c _S_i_m_i_l_a_r_i_t_y _B_e_t_w_e_e_n _T_w_o _G_e_n_e _P_r_o_d_u_c_t_s

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

     Given two Entrez Gene IDs, this function retrieves GO annotation
     and calculates their semantic similarity or distance.

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

     geneSim(gene1, gene2, ont = "MF", measure = "Resnik", drop = NULL, db = "all", multiple = "max")

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

   gene1: Entrez Gene ID 1.

   gene2: Entrez Gene ID 2.

     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 dropped.

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

multiple: Method to be used to combine similarity values if multiple
          terms are associated with a gene product. See description in
          'mtermSim'.

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

    Sim : Semantic similarity or distance value.

    GO1 : Set of terms associated with the first query gene.

    GO2 : Set of terms associated with the second query gene.

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

     'mtermSim' 'termSim'

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

       geneSim("852695", "5261")
       geneSim("852695", "5261", ont="BP", measure="Rel", drop=c("IEA", "ISS"), db="human", multiple="rcmax")

