siggenes2html {siggenes} | R Documentation |
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.
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, ...)
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. See buildSNPannotation for an automatical way to construct
such a data frame given the corresponding metadata package |
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 |
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 |
Holger Schwender, holger.schw@gmx.de
SAM-class
, sam
, EBAM-class
, ebam
,
link.genes
, link.siggenes
, plotArguments
,
plotFindArguments