runOneLayerExtCV-methods       package:Rmagpie       R Documentation

_r_u_n_O_n_e_L_a_y_e_r_E_x_t_C_V: _M_e_t_h_o_d _t_o _r_u_n _a_n _e_x_t_e_r_n_a_l _o_n_e-_l_a_y_e_r _c_r_o_s_s-_v_a_l_i_d_a_t_i_o_n

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

     This method run an external one-layer cross-validation according
     to the options stored in an object of class assessment. The
     concept of external cross-validation has been introduced by G.J.
     McLachlan and C. Ambroise in 'Selection bias in gene extraction on
     the basis of microarray gene-expression data' (cf. section
     References). This technique of cross-validation is used to
     determine an unbiased estimate of the error rate when feature
     selection is involved.

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

  object: 'Object of class assessment'. Object assessment of interest

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

     'object of class assessment' in which the one-layer external
     cross-validation has been computed, therfore, the slot
     'resultRepeated1LayerCV' is no more NULL. This methods print out
     the key results of the assessment, to access the full detail of
     the results, the user must call the method 'getResults'.

_M_e_t_h_o_d_s:


     _o_b_j_e_c_t = "_a_s_s_e_s_s_m_e_n_t" This method is only applicable on objects of
          class assessment.

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

     C. Amboise and G.J. McLachlan 2002. selection bias in gene
     extraction on the basis of microarray gene-expression data. PNAS,
     99(10):6562-6566

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

     'assessment', 'getResults', 'runTwoLayerExtCV-methods'

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

     data('vV70genesDataset')

     # assessment with RFE and SVM
     myExpe <- new("assessment", dataset=vV70genes,
                        noFolds1stLayer=9,
                        noFolds2ndLayer=10,
                        classifierName="svm",
                        typeFoldCreation="original",
                        svmKernel="linear",
                        noOfRepeat=2,
                        featureSelectionOptions=new("geneSubsets", optionValues=c(1,2,3,4,5,6)))

     myExpe <- runOneLayerExtCV(myExpe)

