getFeatureSelectionOptions-methods  package:Rmagpie  R Documentation

_g_e_t_F_e_a_t_u_r_e_S_e_l_e_c_t_i_o_n_O_p_t_i_o_n_s _M_e_t_h_o_d _t_o _a_c_c_e_s_s _t_h_e _a_t_t_r_i_b_u_t_e_s _o_f _a _f_e_a_t_u_r_e_S_e_l_e_c_t_i_o_n_O_p_t_i_o_n_s _f_r_o_m _a_n _a_s_s_e_s_s_m_e_n_t

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

     This method provides an easy interface to access the attributes of
     the object of class featureSelectionOptions related to a
     particular assessment, directly from this object assessment. The
     argument 'topic' specifies which part of the
     featureSelectionOptions is of interest.

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

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

   topic: 'character'. Optional argument that specifies which attribute
          of the featureSelectionOptions is requested, the possible
          values are: '"optionValues"' (Access the slot 'optionValues'
          of the featureSelectionOptions), '"noOfOptions"' (Access the
          slot 'noOfOptions' of the featureSelectionOptions), if the
          featureSelectionOptions object is an object of class
          'geneSubsets', then the following values are also available
          for the argument 'topic'  '"subsetsSizes"' (Access the slot
          'optionValues' of the geneSubsets),  '"noModels"' (Access the
          slot 'noOfOptions' of the geneSubsets),       
          '"maxSubsetSize"' (Access the slot 'maxSelectedFeatures' of
          the geneSubsets), '"speed"' (Access the slot 'speed' of the
          featureSelectionOptions),     if the featureSelectionOptions
          object is an object of class 'thresholds', then the following
          values are also available for the argument 'topic' 
          '"thresholds"' (Access the slot 'optionValues' of the object
          thresholds),  '"noThresholds"' (Access the slot 'noOfOptions'
          of the object thresholds)

          if the 'topic' is missing then the whole
          featureSelectionOptions object is returned.

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

     The value returned by the method changes accordingly to the
     'topic' argument.

     If 'topic' is missing 'object of class featureSelectionOptions'
     the featureSelectionOptions corresponding to the assessment of
     interest

     If 'topic' is "optionValues" 'numeric' corresponding to the
     'optionValues' of the featureSelectionOptions

     If 'topic' is "noOfOptions" 'numeric' corresponding to the
     'noOfOptions' of the featureSelectionOptions

     If 'object' is of class 'geneSubsets' and 'topic' is
     "maxSubsetSize" 'numeric' corresponding to the 'maxSubsetSize'  of
     the geneSubsets

     If 'object' is of class 'geneSubsets' and 'topic' is
     "subsetsSizes" 'numeric' corresponding to the 'optionValues' of
     the geneSubsets  

     If 'object' is of class 'geneSubsets' and 'topic' is "noModels"
     'numeric' corresponding to the 'noOfOptions'  of the geneSubsets

     If 'object' is of class 'geneSubsets' and 'topic' is "speed"
     'numeric' corresponding to the 'speed'  of the geneSubsets  

     If 'object' is of class 'thresholds' and 'topic' is "thresholds"
     'numeric' corresponding to the 'optionValues' of the object of
     class thresholds  

     If 'object' is of class 'thresholds' and 'topic' is "noThresholds"
     'numeric' corresponding to the 'noOfOptions' of the object of
     class thresholds

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


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

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

     Camille Maumet

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

     'featureSelectionOptions', 'assessment'

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

     # With an assessment using RFE
     #dataPath <- file.path("C:", "Documents and Settings", "c.maumet", "My Documents", "Programmation", "Sources", "SVN", "R package", "data")
     #aDataset <- new("dataset", dataId="vantVeer_70", dataPath=dataPath)
     #aDataset <- loadData(aDataset)

     data('vV70genesDataset')

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

     # Return the whole object 'featureSelectionOptions' (an object of class geneSusbsets)
     getFeatureSelectionOptions(myExpe)
     # Size of the biggest subset
     getFeatureSelectionOptions(myExpe, topic='maxSubsetSize')
     # All sizes of subsets
     getFeatureSelectionOptions(myExpe, topic='subsetsSizes')
     # Speed
     getFeatureSelectionOptions(myExpe, topic='speed')
     # Number of subsets
     getFeatureSelectionOptions(myExpe, topic='noModels') == getNoModels(mySubsets)

     # With an assessment using NSC as a feature selection method
     myThresholds <- new("thresholds", optionValues=c(0.1,0.2,0.3))
     myExpe2 <- new("assessment", dataset=vV70genes,
                                        noFolds1stLayer=10,
                                        noFolds2ndLayer=9,
                                        classifierName="nsc",
                                        featureSelectionMethod='nsc',
                                        typeFoldCreation="original",
                                        svmKernel="linear",
                                        noOfRepeat=2,
                                        featureSelectionOptions=myThresholds)

     # Return the whole object 'featureSelectionOptions' (an object of class geneSusbsets)
     getFeatureSelectionOptions(myExpe2)
     # vector of thresholds
     getFeatureSelectionOptions(myExpe2, topic='thresholds')
     # Number of thresholds
     getFeatureSelectionOptions(myExpe2, topic='noThresholds')

