geneSim               package:GOSemSim               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_s

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

     Given two genes, this function will calculate the semantic
     similarity between them,  and return their semantic similarity and
     the corresponding GO terms

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

             geneSim(gene1, gene2, ont = "MF", organism="human",measure="Wang",  drop= "IEA")

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

   gene1: Entrez gene id. 

   gene2: Another entrez gene id.

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

organism: One of "human", "rat", "mouse", "fly" and "yeast".

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

    drop: A set of evidence codes based on which certain annotations
          are dropped. Use NULL to keep all GO annotations.

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

geneSim : Semantic similarity.

    GO1 : Corresponding GO terms for gene1.

    GO2 : Corresponding GO terms for gene2.

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

     Wang et al.(2007) A new method to measure the semantic similarity
     of go terms _Bioinformatics_ (Oxford, England), 23:0 1274-81, May 
     2007. ISSN 1460-2059 <URL:
     http://www.ncbi.nlm.nih.gov/pubmed/17344234> PMID: 17344234

     P W Lord et al.(2003) Semantic similarity measures as tools for
     exploring the gene ontology <URL: Pacific Symposium on
     Biocomputing> Pacific Symposium on Biocomputing, 2003:601-12, ISSN
     1793-5091 <URL: http://www.ncbi.nlm.nih.gov/pubmed/12603061> PMID:
     12603061

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

     'goSim' 'mgoSim' 'mgeneSim' 'clusterSim' 'mclusterSim'

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

             geneSim("241", "2561", ont="MF", organism="human", measure="Wang")
             geneSim("snR18", "YPR062W", ont="MF", organism="yeast", measure="Wang")

