writeToFile            package:arrayMagic            R Documentation

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_a_n_d/_o_r _a_r_r_a_y_D_a_t_a _o_b_j_e_c_t

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

     'writeToFile' generates a well-formated tab-deliminated output
     file of data stored in the 'exprSetRG' and/or 'arrayData' objects.
     Different "views" on either a corresponding pair of an
     'exprSetRG'- and an 'arrayData'-object or of a single object
     itself are possible. The argument 'channels' allows to specify the
     "views". The microarray slide or channel annotation, as well as
     the spot annotation is aligned to the data block if given. For
     further restriction and control of the output, e.g. slide subsets
     or ordering of slides, you may use the subsetting operations
     offered by the 'exprSetRG-class' and 'arrayData-class' beforehand
     (e.g. slideSubset and [] ).

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

     writeToFile(arrayDataObject, exprSetRGObject, additionalDataMatrix, rowSelection, slideNameColumn, channels=c("logRatio"), fileName="dumpedData.txt", savePath=".", fullOutput=TRUE, coding=FALSE)

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

arrayDataObject: object of class 'arrayData'; optional/required, cf.
          'channels'; default: missing

exprSetRGObject: object of class 'exprSetRG'; optional/required, cf.
          'channels'; default: missing

additionalDataMatrix: class 'matrix'; optional; default: missing. The
          rows must correspond to those of the data objects; 'colnames'
          must be supplied.

rowSelection: vector of indexes; optional; default: missing

slideNameColumn: character string; optional; default: missing; must
          refer to a valid column in 'getHybAttr'('arrayDataObject') or
          in 'pDataSlide'('exprSetRGobject') 

channels: vector of character strings; default: 'c("logRatio")'; valid
          character strings are: "logRatio", "green", "red",
          "rawGreen", "rawRed", "rawGreenRelative", "rawRedRelative",
          "se.exprsLogRatio", "se.exprsGreen", "se.exprsRed".
          "Raw"-types must not mix with not "raw"-types and vice versa.
          "logRatio"-types must not mix with "colour"-types. The "raw"
          types require the argument 'arrayDataObject', all other types
          requires at least the argument 'exprSetRGObject'.

fileName: character string; required; default: "dumpedData.txt"

savePath: character string; required; default: "."

fullOutput: logical; adds 'phenoData' information at the top of the
          table ; by default: 'TRUE'

  coding: logical; adds integer-coded-'phenoData' information at the
          top to the table only if 'coding = TRUE' and 'fullOutput =
          TRUE'; default: 'FALSE'

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

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

     The function is called for its side effect, i.e. writing a file.

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

     Andreas Buness <a.buness@dkfz.de>

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

     'exprSetRG-class', 'arrayData-class', 'write.htmltable'

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

       
      

