copaFilter               package:copa               R Documentation

_P_r_e-_f_i_l_t_e_r _G_e_n_e_s _f_o_r _C_O_P_A _A_n_a_l_y_s_i_s

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

     This function is used to pre-filter genes prior to doing a COPA
     analysis. The filtering is based on the nth percentile of the
     outlier samples for each gene. This function is an internal
     function and not intended to be called by the end user.

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

     ## S4 method for signature 'matrix':
     copaFilter(object, cl, cutoff, norm.count, pct)
     ## S4 method for signature 'data.frame':
     copaFilter(object, cl, cutoff, norm.count, pct)
     ## S4 method for signature 'ExpressionSet':
     copaFilter(object, cl, cutoff, norm.count, pct)

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

  object: 

      cl: A vector of classlabels indicating sample status (normal = 1,
          tumor = 2).

  cutoff: The cutoff to determine 'outlier' status. See details for
          more information.

norm.count: The number of normal samples that can be considered
          'outliers'. The default is 0, meaning that no normals may be
          outliers.

     pct: The percentile to use for pre-filtering the data. A
          preliminary step is to compute the number of outlier samples
          for each gene. All genes with a number of outlier samples
          less than the (default 95th) percentile will be removed from
          further consideration.

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

     mat: A matrix containing the gene expression values for the
          filtered genes.

_A_u_t_h_o_r(_s):

     James W. MacDonald

_R_e_f_e_r_e_n_c_e_s:

     Tomlins, SA, et al. Recurrent fusion of TMPRSS2 and ETS
     transcription factor genes in prostate cancer. Science. 2005 Oct
     28;310(5748):644-8.

