siggenes2html            package:siggenes            R Documentation

_H_T_M_L _p_a_g_e _f_o_r _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 html page for a SAM or an EBAM object. This html page
     can contain general information as the number of differentially
     expressed genes and the estimated FDR, the SAM or EBAM plot, and
     gene-specific information on the differentially expressed genes.

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

      ebam2html(object, delta, filename, addStats = TRUE, addPlot = TRUE, 
             addGenes = TRUE, findA0 = NULL, varName = NULL, ll = TRUE, 
             refseq = TRUE, symbol = TRUE, omim = TRUE, ug = TRUE, 
             chipname = "", cdfname = NULL, refsnp = NULL, n.digits = 3, 
             bg.col = "white", text.col = "black", link.col = "blue", 
             plotArgs = plotArguments(), plotFindArgs = plotFindArguments(), 
             bg.plot.adjust = FALSE, plotname = NULL, plotborder = 0, 
             tableborder = 1, new.window = TRUE, ...)

      sam2html(object, delta, filename, addStats = TRUE, addPlot = TRUE, 
             addGenes = TRUE, varName = NULL, ll = TRUE, refseq = TRUE, 
             symbol = TRUE, omim = TRUE, ug = TRUE, chipname = "", 
             cdfname = NULL, refsnp = NULL, n.digits = 3, 
             bg.col = "white", text.col = "black", link.col = "blue", 
             plotArgs = plotArguments(), bg.plot.adjust = FALSE, 
             plotname = NULL, plotborder = 0, tableborder = 1, 
             new.window = TRUE, ...)

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

  object: a SAM or an EBAM object

   delta: a numerical value specifying the Delta value

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

addStats: logical indicating if general information as the number of
          differentially expressed genes and the estimated FDR should
          be added to the html page

 addPlot: logical indicating if the SAM/EBAM plot should be added to
          the html page

addGenes: logical indicating if gene-specific information on the
          differentially expressed genes should be added to the html
          page

  findA0: an object of class FindA0. If specified, the numbers of
          differentially expressed genes and the estimated FDRs for the
          different possible values of the fudge factor and the
          corresponding plot of the logit-transformed posterior
          probabilities are included in the html file

 varName: character string indicating how the variables should be
          named. If 'NULL', the variables will be referred to as SNPs
          in the output if  'method = cat.stat', and as Genes otherwise

      ll: logical indicating if Entrez/Locus Links should be added to
          the output. Ignored if 'addGenes = FALSE'

  refseq: logical indicating if RefSeq links should be added to the
          output. Ignored if 'addGenes = FALSE'

  symbol: logical indicating if the gene symbols should be added to the
          output. Ignored if 'addGenes = FALSE'

    omim: logical indicating if OMIM links should be added to the
          output. Ignored if 'addGenes = FALSE'

      ug: logical indicating if UniGene links should be added to the
          output. Ignored if 'addGenes = FALSE'

chipname: character string specifying the chip type used in the
          analysis. Must be specified as in the meta-data section of
          Bioconductor (e.g., '"hgu133a"' for the Affymetrix HG-U133A
          chip). Need not to be specified if 'cdfname' is specified.
          Ignored if 'addGenes = FALSE'

 cdfname: character string specifying the cdf name of the used chip.
          Must exactly follow the nomenclatur of the Affymetrix chips
          (e.g., '"HG-U133A"' for the Affymetrix HG-U133A chip). If
          specified, links to the Affymetrix webpage for the
          interesting genes will be added to the output. Ignored if
          'addGenes = FALSE'

  refsnp: character vector containing the RefSNP IDs of the SNPs used
          in the SAM/EBAM analysis, where 'names(refsnp)' specifies the
          names of these SNPs

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

  bg.col: specification of the background color of the html page. See
          'par' for how colors can be specified

text.col: specification of the color of the text used in the html page.
          See  'par' for how colors can be specified

link.col: specification of the color of the links used in the html
          file.  See 'par' for how colors can be specified

plotArgs: further arguments for generating the SAM/EBAM plot. These are
          the arguments used by the SAM/EBAM specific 'plot' method.
          See the help of 'plotArguments'  for these arguments. Ignored
          if 'addPlot = FALSE'

plotFindArgs: further arguments for generating the (logit-transformed)
          posterior probabilities for the different values of the fudge
          factor. Ignored if 'findA0 = NULL'. See the help of
          'plotFindArguments' for these arguments

bg.plot.adjust: logical indicating if the background color of the SAM
          plot should be the same as the background color of the html
          page. If 'FALSE' (default) the  background of the plot is
          white. Ignored if 'addPlot = FALSE'

plotname: character string naming the file in which the SAM/EBAM plot
          is stored. This file is needed when the SAM/EBAM plot should
          be added to the html page. If not specified the SAM/EBAM plot
          will be stored as png file in the same folder as the html
          page. Ignored if 'addPlot = FALSE'

plotborder: integer specifying the thickness of the border around the
          plot. By default, 'plotborder = 0', i.e. no border is drawn
          around the plot. Ignored if  'addPlot = FALSE'

tableborder: integer specifying the thickness of the border of the
          table. Ignored if 'addGenes = FALSE'

new.window: logical indicating if the links should be opened in a new
          window

     ...: further graphical arguments for the SAM/EBAM plot. See
          'plot.default' and  'par'. Ignored if 'addPlot = FALSE'

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

     Holger Schwender, holger.schw@gmx.de

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

     'SAM-class', 'sam', 'EBAM-class', 'ebam', 'link.genes',
     'link.siggenes', 'plotArguments', 'plotFindArguments'

