testAnnot               package:BicARE               R Documentation

_F_i_n_d _s_a_m_p_l_e_s _a_n_n_o_t_a_t_i_o_n_s _o_v_e_r-_r_e_p_r_e_s_e_n_t_e_d _c_o_v_a_r_i_a_t_e_s _i_n _b_i_c_l_u_s_t_e_r_s

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

     Characterisation of the biclusters in term of over-representation
     of sample covariates.

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

     testAnnot(resBic, annot=NULL, covariates="all")

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

  resBic: a biclustering result from FLOC

   annot: annotation matrix, default value is set to NULL, then
          phenoData of the ExpressionSet is used

covariates: the names of the covariates that should be tested, default
          value is set to "all"

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

     For each bicluster and each covariate a chi-squarred test is
     performed to test the adequation between the distribution of the
     levels of the covariates in the bicluster and in the original
     dataset.  

     Multiple testing correction is performed by the
     Benjamini-Yekutieli procedure. The residuals of the tests indicate
     if the level is over or down represented in the bicluster.  

     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$covar'.

     The results are presented as a list with :  

   covar: the samples covariates tested

 pvalues: a matrix with the p-values of the tests

adjpvalues: a matrix with the p-values adjusted by the Benjamini
          Yekutieli procedure

   index: a list of matrices with the numbers of each level in each
          bicluster

residuals: a list of matrices with the residuals of the tests for each
          modality in each bicluster

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

     Pierre Gestraud

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

     data(sample.biclustering)
     resBic <- testAnnot(sample.biclustering, annot=NULL, covariates=c("sex", "type"))

