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, entrez = TRUE, 
             refseq = TRUE, symbol = TRUE, omim = FALSE, ug = FALSE,
             fullname = FALSE, chipname = "", cdfname = NULL, 
             which.refseq = "NM", refsnp = NULL, max.associated = 2,
             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, load = TRUE, ...)

      sam2html(object, delta, filename, addStats = TRUE, addPlot = TRUE, 
             addGenes = TRUE, varName = NULL, entrez = TRUE, refseq = TRUE, 
             symbol = TRUE, omim = FALSE, ug = FALSE, fullname = FALSE, 
             bonf = FALSE, chipname = "", cdfname = NULL, which.refseq = "NM", 
             refsnp = NULL, max.associated = 2, 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, load = 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.

  entrez: logical indicating if Entrez 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'.

fullname: logical indicating whether the full gene names should be
          added to the output. Ignored if 'addGenes = FALSE'.

    bonf: logical indicating whether Bonferroni adjusted p-values
          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). Needs not to be specified if 'cdfname' is specified.
          For Affymetrix SNP chips (starting with the 500k array set), 
          'chipname' can be specified by the metadata package name,
          i.e. either by '"pd.genomewidesnp.5"', by
          '"pd.genomewidesnp.6"', by '"pd.mapping250k.nsp"', or by
          '"pd.mapping250k.sty"', to add links to the Affymetrix
          webpage of the SNPs to the html output. 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. If SNP chips
          are considered, 'chipname' instead of 'cdfname' must be
          specified for obtaining these links.  Ignored if 'addGenes =
          FALSE'.

which.refseq: character string or vector naming the first two letters
          of the RefSeq links that should be displayed in the html
          file.

  refsnp: either a character vector or a data frame. If the former,
          'refsnp' containis the RefSNP IDs of the SNPs used in the
          SAM/EBAM analysis, where 'names(refsnp)' specifies the names
          of these SNPs, i.e. their probe set IDs. If a data frame,
          then one column of 'refsnp' must contain the RefSNP IDs of
          the SNPs, and the name of this column must be 'RefSNP'. The
          other columns can contain additional annotations such as the
          chromosome or the physical position of each SNPs. The row
          names of 'refsnp' must specify the SNPs, i.e. must be the
          probe set IDs of the SNPs. Using 'buildSNPannotation' from
          the package 'scrime' such a data frame can be generated
          automatically from the metadata package corresponding to the
          considered SNP chip.

max.associated: integer specifying the maximum number of genes
          associated with the respective SNP displayed in the html
          output. If all entries should be shown, set 'max.associated =
          0'. This however might result in a very large html output.
          For details, see  'shortenGeneDescription' in the package
          'scrime'.

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.

    load: logical value indicating whether to attempt to load the
          required annotation data package if it is not already loaded.
          For details, see the man page of 'lookUp' in the package
          'annotate'.

     ...: 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'

