GetStabilityOverlap       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:

     The similarity of two ordered genelists is assessed by a 'weighted
     cumulative sum' of the number of  overlaps up to a certain
     position in the list and is called 'Overlap Score'. For further
     information, consult the reference given below.

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

     GetStabilityOverlap(RR, decay = c("linear", "quadratic", "exponential"), 
                         scheme = c("rank", "pval"), ...)

_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 overlap score. If 'decay=linear', then we have weight
          '1/s' for rank/p-value 's', if 'decay=quadratic', then the
          weight is '1/s^2' and if 'decay=quadratic', then the weight
          is 'exp(-s*alpha)' where 'alpha' is a tuning parameter,
          specified via the argument 'alpha'

     ...: Currently unused argument.

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

     An object of class GetStabilityOverlap

_N_o_t_e:

     The computed overlap differs from the version described above in
     one point: Here, the overlap score are normalized to fall into the
     unit interval for better interpretability.

_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:

     Lottaz, C., Yang, X., Scheid, S., Spang, R. (2006) 
      OrderedList - a Bioconductor package for detecting similarity in
     ordered gene lists. _Bioinformatics, 22, 2315-2316_

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

     GetRepeatRanking, GetStabilityLm,  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_ov_ordT <- GetStabilityOverlap(loor_ordT, decay="linear")
     ### for a short summary
     summary(stab_ov_ordT)
     ### for a graphical display
     plot(stab_ov_ordT )

