mtermSim               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 _S_e_t_s _o_f _G_O _T_e_r_m_s

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

     Given multiple terms in each query set, semantic similarity is
     taken as the maximum, average, or row/column score combination of
     their pair-wise similarity values.

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

     mtermSim(GO1, GO2, ont, measure = "Resnik", db = "all", multiple = "max")

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

     GO1: First list of GO identifiers.

     GO2: Second list of GO identifiers.

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

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

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

multiple: Methods ("max", "avg", "rcmax") to combine pairwise
          similarity values between two lists of terms.

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

     Gene products are often annotated by multiple terms. The maximum
     or average similarity between all terms associated with two gene
     products may be taken as the gene similarity. For Jiang's distance
     measure, minimum or average value will be taken as the combined
     distance. Alternatively, row score and column score may be
     calculated for the matrix of pairwise similarity values, and the
     maximum (minimum) of these two scores is used as the gene
     similarity (distance).

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

     Semantic similarity or distance between two sets of terms.

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

     Schlicker, A., Domingues, F.S., Rahnenfuhrer, J., and Lengauer, T.
     (2006) A new measure for functional similarity of gene products
     based on Gene Ontology. _BMC Bioinformatics_, 7(1):302.

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

     'termSim'

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

       require(hgu133plus2)

       go1<-sapply(hgu133plus2GO[["203140_at"]], function(x) x$GOID)  
       go2<-sapply(hgu133plus2GO[["208368_s_at"]], function(x) x$GOID)

       mtermSim(go1, go2, ont="CC")
       mtermSim(go1, go2, ont="BP")

