dksCustomClass            package:dualKS            R Documentation

_C_r_e_a_t_e _a _c_l_a_s_s_i_f_i_c_a_t_i_o_n _o_b_j_e_c_t _f_r_o_m _p_r_e_d_e_f_i_n_e_d _g_e_n_e _s_i_g_n_a_t_u_r_e.

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

     This utility function will build a 'DKSClassifier' object  from
     your own list of gene ids for use by 'dksClassify'.  This is
     useful if you want to use the classification funtionality of  this
     package, but already have gene signatures you want to use (as 
     opposed to generating them with 'dksTrain'.

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

     dksCustomClass(upgenes=NULL, upclass=NULL, downgenes=NULL, downclass=NULL)

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

 upgenes: A vector of gene ids that are upregulated in the classes  of
          intereset.  Note that upgenes and downgenes need not both be 
          specified, but at least one must be.

 upclass: A vector or factor of classes specifying which signature 
          each gene in upgenes belongs to.  (Note that upgenes can
          describe  an arbitrary number of classes, and the order of
          upgenes is not  important so long as the position of ids in
          upgenes and the position  of classes in upclass correspond to
          one another).

downgenes: A vector of gene ids that are downregulated in the classes 
          of intereset.  Note that upgenes and downgenes need not both
          be  specified, but at least one must be.

downclass: A vector or factor of classes specifying which signature 
          each gene in downgenes belongs to.  (Note that downgenes can
          describe  an arbitrary number of classes, and the order of
          downgenes is not  important so long as the position of ids in
          downgenes and the position  of classes in downclass
          correspond to one another).

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

     An object of class 'DKSClassifier'.

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

     Eric J. Kort, Yarong Yang

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

     'dksTrain', 'dksSelectGenes', 'dksClassify', 'DKSGeneScores',
     'DKSPredicted',  'DKSClassifier'

_E_x_a_m_p_l_e_s:

             data("dks")
             up <- rownames(exprs(eset))[1:300]
             cls <- factor(rep(c(1,2,3), 100))
             classifier <- dksCustomClass(upgenes=up, upclass=cls)

