RankingTstat          package:GeneSelector          R Documentation

_R_a_n_k_i_n_g _b_a_s_e_d _o_n _t_h_e '_o_r_d_i_n_a_r_y' _t _s_t_a_t_i_s_t_i_c.

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

     Performs univariate (rowwise) t tests on a gene expression matrix.
      For 'S4' method information, see RankingTstat-methods.

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

     RankingTstat(x, y, type = c("unpaired", "paired", "onesample"), pvalues = TRUE, 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, equal variances assumed. 
                For unequal variances, use RankingWelchT.

          "_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.


 pvalues: Should p-values be computed ? Default is 'TRUE'.

gene.names: An optional vector of gene names.

     ...: Currently unused argument.

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

     An object of class GeneRanking.

_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, RankingFC, RankingWelchT, RankingWilcoxon,
     RankingBaldiLong, RankingFoxDimmic, RankingLimma,  RankingEbam,
     RankingWilcEbam, RankingSam,  RankingBstat, RankingShrinkageT,
     RankingSoftthresholdT,  RankingPermutation, 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 RankingTstat
     ordT <- RankingTstat(xx, yy, type="unpaired")

