GetStabilityLm         package:GeneSelector         R Documentation

_S_t_a_b_i_l_i_t_y _m_e_a_s_u_r_e_s _f_o_r _g_e_n_e _r_a_n_k_i_n_g_s

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

     Assesses stability of gene rankings by regressing the rankings of
     perturbed datasets on the ranking of the original datasets in a
     weighted manner. The idea is that if stability is high, the
     resulting regression models fit well.

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

     GetStabilityLm(RR, decay = c("linear", "quadratic", "exponential"), 
                     measure = c("wilks", "direct"), 
                     scheme = c("rank", "pval"), alpha = 1, ...)

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

      RR: An object of class RepeatRanking.

  scheme: Whether ranks ('scheme="rank"') or p-values ('scheme="pval"')
          should be used as basis of weighting.

   decay: argument controlling the weight decay for the weights  used
          in the linear regression model. If 'decay=linear', then the
          weight of the s-th rank/p-value is '1/s', if
          'decay=quadratic', then the weight is '1/s^2' and if
          'decay=exponential', then the weight is 'exp(-s*alpha)',
          where 'alpha' is a tuning parameter specified via the
          argument 'alpha'.

 measure: The stability measure to be computed. If 'measure="wilks"',
          then a stability measure based on the Wilk's Lambda Test for
          multivariate linear regression models is used. If 
          'measure="direct"', then the direct generalization of the
          univariate coefficient of determination to the multivariate
          case is used. The second approach can fail if there exists
          rankings of the perturbed datasets that are exactly equal.

   alpha: To be specified only if 'decay="exponential"', s. also
          GetAlpha.

     ...: Further arguments passed to 'lm'.

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

     An object of class 'GetStabilityLm'

_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:

     Mardia, K.V., Kent, J.T., Bibby, J.M. (1979). 
      Multivariate Analysis _Academic Press._

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

     GetRepeatRanking, GetStabilityOverlap,  RecoveryScore, GetAlpha

_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,]
     ### get ranking 
     ordT <- RankingTstat(xx, yy, type="unpaired")
     ### Generate Leave-One-Out
     loo <- GenerateFoldMatrix(xx, yy, k=1)
     ### Repeat Ranking with t-statistic
     loor_ordT <- GetRepeatRanking(ordT, loo)
     ### assess stability
     stab_lm_ordT <- GetStabilityLm(loor_ordT, decay="linear")
     ### plot
     plot(stab_lm_ordT )

