gseDomain          package:domainsignatures          R Documentation

_G_e_n_e_s_e_t _e_n_r_i_c_h_m_e_n_t _b_a_s_e_d _o_n _I_n_t_e_r_P_r_o _d_o_m_a_i_n _s_i_g_n_a_t_u_r_e_s

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

     Compute the similarity to pathways specified trough 'dataSource'
     for a set of entrezgene identifiers.

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

     gseDomain(dataSource, geneset, n=10000, verbose=TRUE, samples=FALSE)

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

dataSource: Object of class 'ipDataSource' containing pathway and
          InterPro domain mappings

 geneset: Character vector of entrezgene identifiers

       n: Number of subsampling iterations

 verbose: Toggle progress report

 samples: Logical indicating whether to return the similarity measures
          for all the resamples.

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

     Use this function to compute p-values for similarity of the domain
     signature of a gene set to all signatures of the pathways defined
     in 'dataSource'. You should have created 'dataSource' using either
     function 'dataSource' or 'getKEGGdata'.

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

     A list with items

similarity : Named vector of similarity measures for each pathway

 pvalue : The p-values of similarity to each pathway. A named vector.

   dist : A named list containing similarity measures for all the
          resamples

_A_u_t_h_o_r(_s):

     Florian Hahne

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

     'gseDomain'

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

     ## see Vignette of this package for examples how to use this function

