getDataset-methods          package:Rmagpie          R Documentation

_g_e_t_D_a_t_a_s_e_t _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 _d_a_t_a_s_e_t _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
     a dataset directly from an object assessment. The argument 'topic'
     specifies which part of the dataset 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 dataset is requested, the possible values are
          '"dataId"' (slot dataId of the dataset), '"dataPath"' (slot
          dataPath of the dataset), '"geneExprFile"' (slot geneExprFile
          of the dataset), '"classesFile"' (slot classesFile of the
          dataset), '"eset"' (slot eset of the dataset) if the
          '"topic"' is missing then the whole dataset 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 dataset' the dataset
     corresponding to the assessment of interest

     If '"topic"' is '"dataId"' 'object of class character'
     corresponding to the 'dataId' of the dataset

     If '"topic"' is '"dataPath"' 'object of class character'
     corresponding to the 'dataPath' of the dataset

     If '"topic"' is '"geneExprFile"' 'object of class character'
     corresponding to the 'geneExprFile' of the dataset

     If '"topic"' is '"classesFile"' 'object of class character'
     corresponding to the 'classesFile' of the dataset

     If '"topic"' is '"eset"' 'object of class ExpressionSetOrNull'
     corresponding to the 'eset' of the dataset

_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:

     '\code{assessment}'

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

     #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')

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

     getDataset(expeOfInterest)

