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()
     }

