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_n _A_n_n_o_t_a_t_e_d_D_a_t_a_F_r_a_m_e _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 an
     AnnotatedDataFrame 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)
     getOBJWidget(type = NULL)
     objExists(name, type = NULL)
     getSNCNums(sampleNames)
     getCovarDesc(varList)

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

fileName: a character string for the name of a file that is going to be
          used to build an AnnotatedDataFrame object.

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

   pdata: a data.frame for the experimental data.

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

textWidget: an RTcl object for a text box widget.

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

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

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

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

    from: a character string indicating how an AnnotatedDataFrame
          object will be created. "file" - create from an existing
          file, "object" - create from an existing data frame object,
          "edit" - create by editing an existing AnnotatedDataFrame
          object, and "new" create a new AnnotatedDataFrame 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 AnnotatedDataFrame object, the object
     to be imported should have been stored in .GlobelEnv. All the
     objects of data.frame or AnnotatedDataFrame 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. Users have to make sure that Biobase is available.

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

     An AnnotatedDataFrame object.

_N_o_t_e:

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

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

     Jianhua Zhang

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

     AnnotatedDataFrame class in Biobase

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

     'AnnotatedDataFrame-class'

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

     if(interactive()){
         importPhenoData()
     }

