siggenes2html: HTML page for a SAM or an EBAM object

Description

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.

Usage

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, ...)

Arguments

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.

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.

Description

Usage

Arguments

See Also