RepeatRanking-class       package:GeneSelector       R Documentation

"_R_e_p_e_a_t_R_a_n_k_i_n_g"

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

     Object returned by a call to GetRepeatRanking

_S_l_o_t_s:


     '_o_r_i_g_i_n_a_l': The ranking based on the original data set,
          represented by an object of class '"GeneRanking"'

     '_r_a_n_k_i_n_g_s': The rankings obtained from altered datasets, stored as
          a matrix. One column represents one replication. Each column
          is arranged in the same manner as the slot 'ranking' of the
          class 'GeneRanking', i.e. the first entry of a column
          contains the index of the gene ranked highest.

     '_p_v_a_l_s': The p-values obtained from altered data sets, stored
          analogoulsy to 'rankings'. If p-values have not been
          computed, this is a matrix of 'NA's.

     '_s_t_a_t_i_s_t_i_c_s': The statistics obtained from altered data sets,
          stored analogoulsy to 'rankings'

     '_s_c_h_e_m_e': A character for the resampling scheme, can be one of
          '"Subsampling"', '"Labelexchange"', '"Bootstrap"',
          '"Jittering"' (if noise has been added) or '"combined"' if
          several resampling schemes for the same dataset and ranking
          method have been combined via the 'join'-method, s. below.

_M_e_t_h_o_d_s:


     _s_h_o_w use 'show(RepeatRanking-Object)' for brief information.

     _t_o_p_l_i_s_t Use 'toplist(RepeatRanking-Object, k=10)'   to get
          information about the top 'k=10' genes for each replication
          (=perturbed dataset) and one overall table showing
          frequencies of gene indices for each of the ranks '1,...k'. 
          Additionally, only the overall table can be shown with all
          other output suppressed using  'toplist(RepeatRanking-Object,
          show=FALSE)'

     _v_a_r_i_a_n_c_e Genewise variance estimation, s.
          variance,RepeatRanking-method 

     _j_o_i_n use 'join(RepeatRanking-Object1, RepeatRanking-Object2)' to
          combine results from different resampling schemes. The
          results is again an object of class 'RepeatRanking' where the
          slot 'scheme' is '"combined"' and all matrices have been
          concatenated columnwise.

     _p_l_o_t use 'plot(RepeatRanking-Object)' for a scatterplot of
          original rankings and rankings of the perturbed datasets, s.
          plot,RepeatRanking


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

     Martin Slawski martin.slawski@campus.lmu.de 
      Anne-Laure Boulesteix <URL: http://www.slcmsr.net/boulesteix>

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

     GeneRanking, GetRepeatRanking

