MTP-methods             package:multtest             R Documentation

_M_e_t_h_o_d_s _f_o_r _M_T_P _o_b_j_e_c_t_s _i_n _P_a_c_k_a_g_e '_m_u_l_t_t_e_s_t'

_D_e_s_c_r_i_p_t_i_o_n:

     Summary, printing, plotting, subsetting, updating and as.list
     methods were defined for the 'MTP' class. These methods provide
     visual and numeric summaries of the results of a multiple testing
     procedure (MTP) and allow one to perform some basic manipulations
     of an object of class 'MTP'.

_M_e_t_h_o_d_s:



     [ : Subsetting method for 'MTP' class, which operates selectively
          on each slot of an 'MTP' instance to retain only the data
          related to the specified hypotheses.

     _a_s._l_i_s_t : Converts an object of class 'MTP' to an object of class
          'list', with an entry for each slot.

     _p_l_o_t : plot methods for 'MTP' class, produces the following
          graphical summaries of the results of a MTP. The type of
          display may be specified via the 'which' argument. 
           1. Scatterplot of number of rejected hypotheses vs. nominal
          Type I error rate. 

          2. Plot of ordered adjusted p-values; can be viewed as a plot
          of Type I error rate vs. number of rejected hypotheses. 

          3. Scatterplot of adjusted p-values vs. test statistics (also
          known as volcano plot). 

          4. Plot of unordered adjusted p-values. 

          5. Plot of confidence regions for user-specified parameters,
          by default the 10 parameters corresponding to the smallest
          adjusted p-values  (argument 'top'). 

          6. Plot of test statistics and corresponding cut-offs (for
          each value of 'alpha') for user-specified hypotheses, by
          default the 10 hypotheses corresponding to the smallest
          adjusted p-values (argument 'top'). 

          The argument 'logscale' (by default equal to FALSE) allows
          one to use the negative decimal logarithms of the adjusted
          p-values in the second, third, and fourth graphical displays.
          The arguments 'caption' and 'sub.caption' allow one to change
          the titles and subtitles for each of the plots (default
          subtitle is the MTP function call). Note that some of these
          plots are implemented in the older function 'mt.plot'.

     _p_r_i_n_t : print method for 'MTP' class, returns a description of an
          object of class 'MTP', including sample size, number of
          tested hypotheses, type of test performed (value of argument
          'test'), Type I error rate (value of argument 'typeone'),
          nominal level of the test (value of argument 'alpha'), name
          of the MTP  (value of argument 'method'), call to the
          function 'MTP'. 

          In addition, this method produces a table with the class,
          mode, length, and dimension of each slot of the 'MTP'
          instance. 


     _s_u_m_m_a_r_y : summary method for 'MTP' class, provides numerical
          summaries of the results of a MTP and returns a list with the
          following three components. 

          1. rejections: A data.frame with the number(s) of rejected
          hypotheses for the nominal Type I error rate(s) specified by
          the 'alpha' argument of the function 'MTP'. (NULL values are
          returned if all three arguments 'get.cr', 'get.cutoff', and
          'get.adjp' are FALSE). 

          2. index: A numeric vector of indices for ordering the
          hypotheses according to first 'adjp', then 'rawp', and
          finally the absolute value of 'statistic' (not printed in the
          summary). 


          3. summaries: When applicable (i.e., when the corresponding
          quantities are returned by 'MTP'), a table with six number
          summaries of the distributions of the adjusted p-values,
          unadjusted p-values, test statistics, and parameter
          estimates.

_u_p_d_a_t_e : update method for 'MTP' class, provides a mechanism to re-run
     the MTP with different choices of the following arguments -
     alternative, typeone, k, q, fdr.method, alpha, smooth.null,
     method, get.cr, get.cutoff, get.adjp, keep.nulldist. When evaluate
     is 'TRUE', a new object of class MTP is returned. Else, the
     updated call is returned. The 'MTP' object passed to the update
     method must have a non-empty nulldist slot (ie: must have been
     called with 'keep.nulldist=TRUE'). 

_A_u_t_h_o_r(_s):

     Katherine S. Pollard with design contributions from Sandrine
     Dudoit and Mark J. van der Laan.

