siggenes2html(siggenes)
siggenes2html()所属R语言包：siggenes
HTML page for a SAM or an EBAM object
为SAM或EBAM的对象的HTML页
译者：生物统计家园网 机器人LoveR
描述----------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.
为SAM或EBAM的对象生成一个HTML页面。这个HTML页面可以包含差异表达的基因数目和估计FDR，SAM或EBAM图，特定基因的差异表达基因信息的一般信息。
用法----------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, ...)
参数----------Arguments----------
参数：object
a SAM or an EBAM object.
一个SAM或EBAM对象。
参数：delta
a numerical value specifying the Delta value.
指定的Delta值的数值。
参数：filename
character string naming the file in which the output should be stored. Must have the suffix ".html".
字符串命名应存放在输出的文件。必须有后缀“HTML”。
参数：addStats
logical indicating if general information as the number of differentially expressed genes and the estimated FDR should be added to the html page.
逻辑表示如果作为一般信息的差异表达基因和估计FDR应该被添加到HTML页面。
参数：addPlot
logical indicating if the SAM/EBAM plot should be added to the html page
逻辑表明，如果SAM / EBAM图应该被添加到HTML页面
参数：addGenes
logical indicating if gene-specific information on the differentially expressed genes should be added to the html page.
逻辑表示应增加特定基因的差异表达基因信息的HTML页面。
参数：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.
一个类FindA0对象。如果指定，差异表达的基因，并为不同的可能值的软糖因素和相应的图“的罗吉特转化的后验概率的估计FDRs的数字是包含在HTML文件中。
参数：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.
字符串，指示如何应命名的变量。如果NULL，变量将被称为输出为单核苷酸多态性，如果method = cat.stat，否则作为基因。
参数：entrez
logical indicating if Entrez links should be added to the output. Ignored if addGenes = FALSE.
Entrez的链接应该被添加到输出逻辑指示。如果addGenes = FALSE忽略。
参数：refseq
logical indicating if RefSeq links should be added to the output. Ignored if addGenes = FALSE.
逻辑指示应被添加到输出的RefSeq链接。如果addGenes = FALSE忽略。
参数：symbol
logical indicating if the gene symbols should be added to the output. Ignored if addGenes = FALSE.
逻辑表明，如果基因符号应该被添加到输出。如果addGenes = FALSE忽略。
参数：omim
logical indicating if OMIM links should be added to the output. Ignored if addGenes = FALSE.
OMIM链接应该被添加到输出逻辑表示。如果addGenes = FALSE忽略。
参数：ug
logical indicating if UniGene links should be added to the output. Ignored if addGenes = FALSE.
逻辑表示如果UniGene的链接应该被添加到输出。如果addGenes = FALSE忽略。
参数：fullname
logical indicating whether the full gene names should be added to the output. Ignored if addGenes = FALSE.
逻辑指示是否应该被添加到输出的完整的基因名称。如果addGenes = FALSE忽略。
参数：bonf
logical indicating whether Bonferroni adjusted p-values should be added to the output. Ignored if addGenes = FALSE.
应添加到输出逻辑指示是否邦弗朗尼调整p值。如果addGenes = FALSE忽略。
参数：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.
字符串指定在分析中使用的芯片类型。必须指定为Bioconductor元数据部分（例如，"hgu133a"Affymetrix公司的HG-U133A芯片）。需要不被指定，如果cdfname指定。 Affymetrix公司的SNP芯片（500K阵列集开始），chipname可以通过指定的元数据包名称，即\要么"pd.genomewidesnp.5"由"pd.genomewidesnp.6"，"pd.mapping250k.nsp"，或"pd.mapping250k.sty"，Affymetrix公司的SNP网页链接添加到HTML输出。如果addGenes = FALSE忽略。
参数：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.
字符串指定所使用的芯片的CDF名称。必须严格遵循的Affymetrix芯片nomenclatur（例如，"HG-U133A"Affymetrix公司的HG-U133A芯片）。如果指定的，有趣的基因的Affymetrix公司的网页链接将被添加到输出。如果被认为是SNP的芯片，chipname而不是cdfname必须获得这些链接指定。如果addGenes = FALSE忽略。
参数：which.refseq
character string or vector naming the first two letters of the RefSeq links that should be displayed in the html file.
字符串或向量命名的前两个字母的，应在HTML文件中显示的RefSeq链接。
参数：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.
无论是字符向量或一个数据框。如果是前者，refsnpcontainis SAM / EBAM分析中使用的SNPs，其中names(refsnp)指定这些SNPs的名称，即\自己的探针集ID RefSNP标识。如果一个数据框，然后一列必须包含refsnp的SNP RefSNP标识，此列的名称必须是RefSNP。其他列可以包含额外的注释，如染色体或每个单核苷酸多态性的物理位置。 \refsnp行名称必须指定的单核苷酸多态性，即必须是探针的SNP集ID。使用buildSNPannotation包scrime这样一个数据框可以自动生成元数据包对应考虑的SNP芯片。
参数：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.
整数，指定的HTML输出中显示各自的单核苷酸多态性与相关基因的最大数量。如果所有参赛作品应显示，设置max.associated = 0。然而，这可能会导致一个非常大的HTML输出。有关详细信息，请参阅shortenGeneDescription包scrime的。
参数：n.digits
integer specifying the number of decimal places used in the output.
整数，指定在输出中使用的小数。
参数：bg.col
specification of the background color of the html page. See par for how colors can be specified.
规范的HTML页面的背景颜色。看到par如何可以指定颜色的。
参数：text.col
specification of the color of the text used in the html page. See par for how colors can be specified.
在HTML页面中使用的文本的颜色规范。看到par如何可以指定颜色的。
参数：link.col
specification of the color of the links used in the html file. See par for how colors can be specified.
规范用于在HTML文件中的链接的颜色。看到par如何可以指定颜色的。
参数：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.
SAM / EBAM图产生进一步的论据。这些都是由SAM / EBAM具体plot方法使用的参数。看到plotArguments这些参数的帮助。如果addPlot = FALSE忽略。
参数：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.
蒙混因素的不同值的后验概率（罗吉特转化）产生进一步的论据。如果findA0 = NULL忽略。看到plotFindArguments这些参数的帮助。
参数：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.
逻辑表明，如果SAM的图背景颜色应该是作为HTML页面的背景颜色相同。如果FALSE（默认）图的背景是白色的。如果addPlot = FALSE忽略。
参数：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.
字符串命名的文件存储在SAM / EBAM图。 SAM / EBAM图时，应添加到HTML页面，这个文件是必要的。如果没有指定的SAM / EBAM图将被保存为png文件在同一文件夹中的HTML页面。如果addPlot = FALSE忽略。
参数：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.
整数，指定边框的厚度，周围的图。默认情况下，plotborder = 0，即\绘制无边框周围的图。如果addPlot = FALSE忽略。
参数：tableborder
integer specifying the thickness of the border of the table. Ignored if addGenes = FALSE.
整数，指定表格边框的厚度。如果addGenes = FALSE忽略。
参数：new.window
logical indicating if the links should be opened in a new window.
逻辑指示应在新窗口中打开链接。
参数：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.
逻辑值指示是否尝试加载所需的注释数据包，如果它尚未被载入。有关详情，请参阅lookUp包annotate手册页。
参数：...
further graphical arguments for the SAM/EBAM plot. See plot.default and par. Ignored if addPlot = FALSE.
为进一步的SAM / EBAM图图形参数。看到plot.default和par。如果addPlot = FALSE忽略。
作者（S）----------Author(s)----------
Holger Schwender, <a href="mailto:holger.schw@gmx.de">holger.schw@gmx.de</a>
参见----------See Also----------
SAM-class, sam, EBAM-class, ebam, link.genes, link.siggenes, plotArguments, plotFindArguments
SAM-class，sam，EBAM-class，ebam，link.genes，link.siggenes，plotArguments，plotFindArguments
转载请注明:出自 生物统计家园网(http://www.biostatistic.net)。
注：
注1：为了方便大家学习，本文档为生物统计家园网机器人LoveR翻译而成，仅供个人R语言学习参考使用，生物统计家园保留版权。
注2：由于是机器人自动翻译，难免有不准确之处，使用时仔细对照中、英文内容进行反复理解，可以帮助R语言的学习。
注3：如遇到不准确之处，请在本贴的后面进行回帖，我们会逐渐进行修订。
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发表于 2012-2-26 14:15:39
