importPhenoData          package:tkWidgets          R Documentation

_F_u_n_c_t_i_o_n_s _t_o _i_n_p_u_t _d_a_t_a _f_o_r _a _p_h_e_n_o_D_a_t_a _o_b_j_e_c_t

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

     This functions allow users to read data from an existing file or
     an R data frame object and use the data frame to construct a
     phenoData object

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

     importPhenoData(fileName, sampleNames = NULL, from = NULL)
     createPData(pdata, varList)
     writePDRowNames(pdata, sampleNames)
     writePhenoTable(base, textWidget, pdata)
     makePhenoData(pdata)
     convert2PData(phenoList)
     getPDFromFile()
     getOBJWidget(type = NULL)
     objExists(name, type = NULL)
     getSNCNums(sampleNames)
     getCovarDesc(varList)

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

fileName: 'fileName' a character string for the name of a file that is
          going to be used to build a phenoData object

sampleNames: 'sampleNames' a vector of character strings for the names
          of samples. The length of 'smapleNames' should be the same as
          the number of rows of an existing file or data frame if a
          phenoData object is to be created based on a file or data
          frame

   pdata: 'pdata' a data frame for the experimental data

    base: 'base' an RTcl object for the base window a widget resides

textWidget: 'textWidget' an RTcl object for a text box widget

phenoList: 'phenoList' a list of lists for tclVar() objects

    type: 'type' a character string for the class of a object e. g.
          data.frame, phenoData

    name: 'name' a character string for the name of an object

 varList: 'varList' a list of characters with names being coavraite
          names and values being short descriptions of covariate names

    from: 'from' a character string indicating hwo a phenoData object
          will be created. "file" - create from an existing file,
          "object" - create from an existing data frame object, "edit"
          - create by editing an existing phenoData object, and "new"
          create a new phenoData object from scratch. NULL or any other
          values for 'from' will invoke a widget that allows users to
          select one of the four means from an interface

_D_e_t_a_i_l_s:

     When import a data frame or phenoData object, the object to be
     imported should have been stored in .GlobelEnv. All the objects of
     data frame or phenoData will be made available through a browser.

     The main widget if 'importPhenoData' that calls other
     functions/widgets to have the job done.

     Package Biobase is required for importPhenoData but the
     requirement id not forced as it is the only time the package is
     used. Uers have to make sure that Biobase is available.

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

     A phenoData object

_N_o_t_e:

     This function is intended for use by funciton read.phenoData of
     Biobase

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

     Jianhua Zhang

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

     phenoData class in Biobase

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

     if(interactive()){
         importPhenoData()
     }

