RankingGap           package:GeneSelector           R Documentation

_R_a_n_k_i_n_g _b_a_s_e_d _o_n '_g_a_p_s'

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

     The ranking is based on the _gap_ between two classes (for
     'type="unpaired"') where the gap is defined as 'gap(1,2) =
     max(min2 - max1, min1-max2, 0)', where min1, max1 are the
     minimum/maximum observed values from class 1 (analogously for
     min2, max2). It is only greater than zero if classes do not
     overlap. For 'type="paired", "onesample"' the gap, i.e. absolute
     distance from the origin is computed.
      For 'S4' method information, see RankingFC-methods.

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

     RankingGap(x, y, type = c("unpaired", "paired", "onesample"), 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'.
           If 'type = paired', the first half of the columns
          corresponds to  the first measurements and the second half to
          the second ones.  For instance, if there are 10 observations,
          each measured twice, stored in an expression matrix 'expr', 
          then 'expr[,1]' is paired with 'expr[,11]', 'expr[,2]' with
          'expr[,12]', and so on.

       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'.
           If 'type = paired', take care that the coding is analogously
          to the requirement concerning 'x'


          "_u_n_p_a_i_r_e_d": two-sample test.

          "_p_a_i_r_e_d": paired test. Take care that the coding of 'y' is
               correct (s. above)

          "_o_n_e_s_a_m_p_l_e": 'y' has only one level.  Test whether the true
               mean is different from zero.

gene.names: An optional vector of gene names.

     ...: Currently unused argument.

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

     An object of class GeneRanking.

_N_o_t_e:

     In most cases, classes will not be separated by only one gene.
     Consequently, the great majority of statistics will be zero.
      p-values are _not_ available.

_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:

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

_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 RankingGap
     gapstat <- RankingGap(xx, yy, type="unpaired")

