readMageDesign            package:MAGEML            R Documentation

_W_r_a_p_p_e_r _f_u_n_c_t_i_o_n _f_o_r _r_e_a_d_i_n_g _M_A_G_E-_M_L _d_o_c_u_m_e_n_t_s

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

     The function 'readMageDesign' is a wrapper function for reading
     MAGE-ML documents. It returns objects of the classes 
     'marrayLayout' and 'marrayInfo'.

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

     readMageDesign(file = NULL, datadir = ".",  fArrayDesign = NULL, fBioAssayData = NULL, fDesignElement = NULL, fBioSequence = NULL, ngc=4, skip=0, sep="\t",quote="",...)

     widget.readMageDesign(skip=0, sep="\t",quote="",...)

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

fArrayDesign: Filename of XML document containing the ArrayDesign
          package.

fBioAssayData: Filename of XML document containing the BioAssayData
          package.

fDesignElement: Filename of XML document containing the DesignElement
          package.

fBioSequence: Filename of XML document containing the BioSequence
          package.

    file: Filename of XML document when the ArrayDesign, BioassayData
          and DesignElement package are all in one XML file.

 datadir: Directory containing the XML document

     ngc: The number of grid columns on your array; the default is 4.

     ...: Further arguments for the `scan' function

    skip: Further arguments for the `scan' function

   quote: Further arguments for the `scan' function

     sep: Further arguments for the `scan' function

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

     This function executes an event based XML parsing.  Depending on
     whether the ArrayDesign, BioAssayData and DesignElement package
     are in one file or not, three different files will be parsed or
     only one.

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

     A marrayLayout an a marrayInfo object, named layout and info.

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

     Joke Allemeersch, <URL: http://www.esat.kuleuven.ac.be/~jallemee>
      Steffen Durinck, <URL: http://www.esat.kuleuven.ac.be/~sdurinck>.

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

     Spellman PT, Miller M, Stewart J, Troup C, Sarkans U, Chervitz S,
     Bernhart D, Sherlock G, Ball C, Lepage M, Swiatek M, Marks WL,
     Goncalves J, Markel S, Iordan D, Shojatalab M, Pizarro A, White J,
     Hubley R, Deutsch E, Senger M, Aronow BJ, Robinson A, Bassett D,
     Stoeckert CJ Jr and Brazma A. Design and implementation of
     microarray gene expression markup language (MAGE-ML). Genome Biol.
     2002 Aug 23;3(9):RESEARCH0046.

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

     'getBioAssayData', 'getDesignElement','getArrayDesign'.

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

     data <- system.file("data", package="MAGEML")
     readMageDesign(file = "Iron.xml", datadir = data)
     #To call the widget, you use:
     if(interactive()){
     widget.readMageDesign()
     }

