RankingPermutation       package:GeneSelector       R Documentation

_R_a_n_k_i_n_g _b_a_s_e_d _o_n _p_e_r_m_u_t_a_t_i_o_n _t_e_s_t_s.

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

     The function is a wrapper for 'mt.sample.teststat' from the
     package 'multtest' (Dudoit et al, 2003). The ranking is here based
     on permutation p-values first, followed by the absolute value of
     the statistic. For 'S4' method information, see
     RankingPermutation-methods.

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

     RankingPermutation(x, y, type = "unpaired", B = 100, gene.names = NULL, ...)

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

       x: A 'matrix' of gene expression values with rows corresponding
          to genes and columns corresponding to observations or
          alternatively an object of class 'ExpressionSet'.

       y: If 'x' is a matrix, then 'y' may be a 'numeric' vector or a
          factor with at most two levels.
           If 'x' is an 'ExpressionSet', then 'y' is a character
          specifying the phenotype variable in the output from 'pData'.

    type: Only the two sample case, 'type="unpaired"' is possible.

       B: The number of permutations to generate. Defaults to 100, but
          should be increased if computing power admits. Taking 'B' too
          high, however, can lead to long computation time, especially
          if called from GetRepeatRanking

gene.names: An optional vector of gene names.

     ...: Further arguments passed to 'mt.sample.teststat' from the
          package 'multtest'. Can be used, for example, to select the
          statistic to be computed. By default this is '"t.equalvar"'
          (t-test with equal variances assumed).

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

     An object of class 'GeneRanking'

_N_o_t_e:

     The p-values, on which the ranking is primarily based, suffer from
     the discreteness of the procedure. They follow a step function
     with jump heights '1/B'.

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

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

_R_e_f_e_r_e_n_c_e_s:

     Dudoit, S., Shaffer, J.P., Boldrick, J.C. (2003). 
       Multiple Hypothesis Testing in Microarray Experiments
     _Statistical Science, 18, 71-103_

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

     GetRepeatRanking, RankingTstat, RankingFC, RankingWelchT,
     RankingWilcoxon, RankingBaldiLong, RankingFoxDimmic, RankingLimma,
      RankingEbam, RankingWilcEbam, RankingSam,  RankingBstat,
     RankingShrinkageT, RankingSoftthresholdT,  RankingGap

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

     ### Load toy gene expression data
     data(toydata)
     ### class labels
     yy <- toydata[1,]
     ### gene expression
     xx <- toydata[-1,]
     ### run RankingPermutation (100 permutations)
     perm <- RankingPermutation(xx, yy, B=100, type="unpaired")

