testSet                package:BicARE                R Documentation

_F_i_n_d _g_e_n_e _s_e_t_s _t_h_a_t _a_r_e _e_n_r_i_c_h_e_d _i_n _a _b_i_c_l_u_s_t_e_r

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

     Test of the over-representation of gene sets in the biclusters

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

     testSet(resBic, geneSetCol)

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

  resBic: a 'biclustering' object created by 'FLOC'

geneSetCol: a 'GeneSetCollection-class'

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

     The over-representation of a gene set in a bicluster is evaluated
     by an hypergeometric test. 

     The genes identifiers of the gene sets will automatically be
     mapped to the same as those used in the data. 

     Due to the amount of results it is advised to use the 'makeReport'
     function to get a html report.

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

     A 'biclustering' object containing 'resBic' and updated with the
     results of the tests in 'resBic$geneSet'.

     The results are presented as a list with :  

GeneSetCollection: the GeneSetCollection used

 pvalues: a matrix containing the pvalues of the tests for each geneSet
          and each bicluster

adjpvalue: a matrix containing the p-values adjusted by the Benjamini
          Yekutieli procedure

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

     Pierre Gestraud pierre.gestraud@curie.fr

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

     data(sample.biclustering)
     gss <- GeneSetCollection(sample.biclustering$ExpressionSet[1:50,], setType=GOCollection())
     resBic <- testSet(sample.biclustering, gss)

