test.overrepresentation     package:gene2pathway     R Documentation

_T_e_s_t _s_t_a_t_i_s_t_i_c_a_l _o_v_e_r_r_e_p_r_e_s_e_n_t_a_t_i_o_n _o_f _K_E_G_G _p_a_t_h_w_a_y_s _i_n _a _l_i_s_t _o_f _g_e_n_e_s

_D_e_s_c_r_i_p_t_i_o_n:

     Test the statistical overrepresentation of KEGG pathways in a
     group of genes using Fisher's exact test. The analysis can either
     be based on all KEGG pathways predicted by
     'gene2pathway'/'gene2pathway.signaltrans' or on original KEGG
     annotation only.

_U_s_a_g_e:

     test.overrepresentation(genesOfInterest, predpath, KEGGonly=FALSE, cutoff=0.1, min.conf=0.9, adj.method="BY")

_A_r_g_u_m_e_n_t_s:

genesOfInterest: a character vector of gene identifiers (see
          'gene2pathway', 'gene2pathway.signaltrans') for a gene list
          of interest

predpath: predictions of 'gene2pathway' or 'gene2pathway.signaltrans'

KEGGonly: use KEGG annotation only

  cutoff: p-value significance cutoff

min.conf: filter predictions such that only those with a confidence
          score > min.conf are considered

adj.method: multiple testing correction method. Default:
          Benjamini-Yekutieli

_V_a_l_u_e:

     Table with two columns: KEGG pathway and adjusted p-value
     (adjustment according to Benjamini-Yekutieli)

