siggenes2excel           package:siggenes           R Documentation

_C_S_V _f_i_l_e _o_f _a _S_A_M _o_r _a_n _E_B_A_M _o_b_j_e_c_t

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

     Generates a csv file for either a SAM or an EBAM object for the
     use in Excel. This csv file can contain  general information as
     the number of differentially expressed genes and the estimated
     FDR, and gene-specific information on the differentially expressed
     genes.

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

      sam2excel(object, delta, file, excel.version=1, n.digits = 3, what = "both", ll = FALSE,
             chip = "", quote = FALSE)
             
      ebam2excel(object, delta, file, excel.version=1, n.digits = 4, what = "both", ll = FALSE,
             chip = "", quote = FALSE)

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

  object: either a SAM or an EBAM object

   delta: a numerical value specifying the Delta value

    file: character string naming the file in which the output should
          be stored. Must have the suffix ".csv"

excel.version: either '1' or '2'. If 'excel.version=1' (default) a csv
          file for the use in an Excel version with American standard
          settings ('sep=","' and  'dec="."') will be generated. If
          'excel.version=2' a csv file for the European standard
          setting ('sep=";"' and 'dec=","') will be generated

n.digits: integer specifying the number of decimal places used in the
          output

    what: either '"both"', '"stats"' or '"genes"'. If '"stats"' general
           information will be shown. If '"genes"' gene-specific
          information will be given.  If '"both"' both general and
          gene-specific information will be shown

      ll: logical indicating if both the locus links and the symbols of
          the genes will be added to the output

    chip: character string naming the chip type used in this analysis.
          Must be specified as in the meta-data section of Bioconductor
          (e.g., '"hgu133a"' for the Affymetrix HG-U133A chip). Only
          needed if 'll=TRUE'.  If the argument 'data' in 'sam(data,
          cl, ...)' has been specified  by an 'ExpressionSet' object
          'chip' need not to be specified

   quote: logical indicating if character strings and factors should be
          surrounded by  double quotes. For details see 'write.table'

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

     Holger Schwender, holger.schw@gmx.de

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

     'sam', 'sam2html', 'ebam', 'ebam2html'

