GetStabilityGLM         package:GeneSelector         R Documentation

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

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

     Assesses the stability of the set of genes declared statistically
     significant for differential expression. To this end, p-values or
     adjusted p-values are used to generate binary response variables
     for a logistic regression model. As single covariate, the ranks
     obtained from the original dataset are used. Analogously to the
     linear model approach, weights are incorporated to attribute more
     importance to higher ranked genes. The deviance(s) resulting from
     these models are used as stability measure.

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

     GetStabilityGLM(RR, decay = c("linear", "quadratic", "exponential"),
                     scheme = c("rank", "pval"), alpha = 1,
                     maxpval = 0.05, method=c("raw", "BH", "qvalue", "Bonferroni", "Holm", "Hochberg", "SidakSS", "SidakSD", "BY"))

_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'.

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

 maxpval: The maximum p-value that is still considered significant
          (type I error). Default is 0.05.

  method: The method used for p-value adjustment, s. AdjustPvalues. If
          'method = "raw"', then the raw p-values will be used.

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

     An object of class 'GetStabilityGLM'

_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, GetStabilityLm, GetStabilityOverlap,
     GetStabilityPCA, RecoveryScore, GetAlpha

