sam2html              package:siggenes              R Documentation

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

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

      sam2html(sam.out, delta, filename, addStats = TRUE, addPlot = TRUE, addGenes = TRUE,
             ll = TRUE, refseq = TRUE, symbol = TRUE, omim = TRUE, ug = TRUE,
             chipname = "", cdfname = 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:

 sam.out: a SAM 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 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

      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'

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 plot. These are the
          arguments used by 'sam.plot2' and 'plot', respectively. See
          '?plotArgs' for these arguments. Ignored if 'addPlot=FALSE'

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 plot is
          stored. This file is needed when the SAM plot should be added
          to the html page. If not specified the SAM 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 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', 'link.genes', 'link.siggenes', 'sam2excel',
     'plotArguments'

