writeReport(cellHTS2)
writeReport()所属R语言包：cellHTS2
Create a directory with HTML pages of linked tables and plots
创建HTML页面的链接表和图目录
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Creates a directory with HTML pages of linked tables and plots
创建HTML页面的链接表和图目录
用法----------Usage----------
writeReport(
raw,
normalized=NULL,
scored=NULL,
cellHTSlist=NULL,
outdir,
force=FALSE,
map=FALSE,
plotPlateArgs=NULL,
imageScreenArgs=NULL,
posControls,
negControls,
mainScriptFile=NA,
gseaModule=NULL,
settings=list())
参数----------Arguments----------
参数：raw
the intitial raw cellHTS object. See details.
在intitial原料cellHTS对象。查看详情。
参数：normalized
a normalized cellHTS object. See details.
归一cellHTS对象。查看详情。
参数：scored
a scored cellHTS object. See details.
1拿下cellHTS对象。查看详情。
参数：cellHTSlist
a list of cellHTS objects. See details. Note: this argument is deprecated. Please use the separate arguments raw, normalized and scored instead.
cellHTS对象名单。查看详情。注：这种说法已经过时了。请使用单独的参数raw，normalized和scored代替。
参数：outdir
a character of length 1 with the name of a directory where to write the report HTML file and images. If the directory does not exist, it is created. If it exists and is not empty, then the behaviour depends on the value of force. If outdir is missing, it is set to file.path(getwd(), name(cellHTSlist[['xraw']])), i.e. a directory with the name of the cellHTS object(s) in the current working path.
字符的目录的名称写报告HTML文件和图像的长度1。如果该目录不存在，则创建它。如果它存在，并且不为空，则行为取决于上force值。如果outdir缺少，它被设置为file.path(getwd(), name(cellHTSlist[['xraw']]))，即用的cellHTS的对象，在当前的工作路径（S）的名称的目录。
参数：force
a logical value, determines the behaviour of the function if outdir exists and is not empty. If force is TRUE, the function overwrites (removes and recreates) outdir, otherwise it casts an error.
一个逻辑值，决定如果outdir存在，并且不为空的函数的行为。 force如果是TRUE，功能覆盖（删除并重新创建）outdir，否则施放的错误。
参数：map
a logical value indicating whether tooltips with the annotation should be added to the plate plots and image screen. Default value is FALSE. NOTE: This argument is deprecated and will go away in the next release. Please see settings to learn how to control the output of writeReport.
一个逻辑值，该值指示是否应加注释的工具提示板图和影像画面。默认值为FALSE。注：这种说法已经过时，将在下一个版本中。请看到settings学习如何控制writeReport的输出。
参数：plotPlateArgs
either a list with parameters for the plate plots of the per plate quality report pages, or a logical scalar with values FALSE or TRUE. If FALSE or NULL, the plate plots are omitted, this option is here because the production of the plate plots takes a long time. See details. NOTE: This argument is deprecated and will go away in the next release. Please see settings to learn how to control the output of writeReport.
无论是板每板质量报告页面图列表参数，或与逻辑标值FALSE或TRUE。如果FALSE或NULL，板块图被忽略，此选项是在这里生产的板图，因为需要较长的时间。查看详情。注：这种说法已经过时，将在下一个版本中。请看到settings学习如何控制writeReport的输出。
参数：imageScreenArgs
a list with parameters for the function imageScreen. See details. NOTE: This argument is deprecated and will go away in the next release. Please see settings to learn how to control the output of writeReport.
与功能imageScreen参数列表。查看详情。注：这种说法已经过时，将在下一个版本中。请看到settings学习如何控制writeReport的输出。
参数：posControls
a list or vector of regular expressions specifying the name of the positive controls. See details.
正则表达式指定的阳性对照的名称列表或向量。查看详情。
参数：negControls
a vector of regular expressions specifying the name of the negative controls. See details.
一个正则表达式的向量指定名称的阴性对照。查看详情。
参数：mainScriptFile
The path to the R script generating the current report. We strongly advice to store this script in the compendium for future reference.
产生的电流的报告的R脚本的路径。我们强烈建议储存在汇编，以供将来参考该脚本。
参数：gseaModule
Add the output of a gene set enrichment analysis to the report. This is totally experimental at this time.
添加一个基因组富集分析报告输出。此时，这完全是实验。
参数：settings
A named list of settings controlling the output of writeReport. Please see settings for details.
命名的设置控制writeReport的输出列表。请参阅settings详情。
Details
详情----------Details----------
The function has to be called with the mandatory argument raw corresponding to an unnormalized cellHTS object (i.e. state(cellHTSlist[["raw"]])["normalized"]=FALSE). Additional optional arguments are:
被称为强制性参数raw对应一个非标准化的cellHTS对象的功能（即state(cellHTSlist[["raw"]])["normalized"]=FALSE）。额外的可选参数是：
"normalized": a cellHTS object containing normalized data (i.e. state(cellHTSlist[["normalized"]])["normalized"]=TRUE and state(cellHTSlist[["normalized"]])["scored"]=FALSE).
"normalized"：cellHTS对象，其中包含规范化的数据（即state(cellHTSlist[["normalized"]])["normalized"]=TRUE和state(cellHTSlist[["normalized"]])["scored"]=FALSE）。
"scored": a cellHTS object containing data scored data (i.e. state(cellHTSlist[["scored"]])["scored"]=TRUE). If this component is available, then cellHTSlist[["normalized"]] should also be given.
"scored"：cellHTS对象，它包含数据的得分数据（即state(cellHTSlist[["scored"]])["scored"]=TRUE）。如果此组件是可用的，那么cellHTSlist[["normalized"]]也应该得到。
All of the above arguments have to be cellHTS objects containing data from the same experiment, but in different preprocessing stages.
所有上述论点是cellHTS含有相同的实验数据的对象，但在不同的预处理阶段。
The cellHTS argument is deprecated and should no be used anymore.
cellHTS参数已被废弃，不应该再使用。
The following elements are recognized for plotPlateArgs and passed on to plotPlate: sdcol, the color scheme for the standard deviation plate plot, sdrange, the sd range to which the colors are mapped, xcol, the color scheme for the intensity plate plot, xrange, the intensity range to which the colors are mapped. If an element is not specified, default values are used. Both sdrange and xrange can also be provided as functions, which take the values to be plotted by platePlot as a single argument and has to return a numeric vector of length 2. See its documentation for details.
以下元素被确认为plotPlateArgsplotPlate：sdcol，标准偏差板图的配色方案，sdrange，SD系列，颜色，并通过对映射，xcol，强度钢板图的配色方案，xrange，强度范围的颜色映射。如果一个元素没有被指定，则使用默认值。既sdrange和xrange值绘制的功能，也可作为提供platePlot作为一个参数，并返回一个长度为2的数字向量。看到它的详细信息的文档。
The following elements are recognized for imageScreenArgs and passed on to imageScreen: ar, aspect ratio, zrange, range, anno, gene annotation for the image map (if map=TRUE).
下列元素被确认为imageScreenArgs，并通过imageScreen：ar，长宽比，zrange，范围，anno，基因注释的影像图（如果map=TRUE）。
From now on, all settings controlling the output of writeReport should either be provided through the settings argument, or as session-wide parameters set using setSettings. Please see settings for details.
从现在开始，所有的设置控制writeReport输出应该既可以通过settings参数，或会话范围的参数设置使用setSettings。请参阅settings详情。
posControls and negControls should be given as a vector of regular expression patterns specifying the name of the positive(s) and negative(s) controls, respectivey, as provided in the plate configuration file (and acccessed via wellAnno(objects)).
posControls和negControls应指定名称（S）的积极和消极的（S）控制，respectivey板的配置文件（提供正则表达式模式的向量和acccessed的通过wellAnno(objects)）。
If the cellHTS object containing normalized data was provided as argument norm, the length of posControls and negControls should be equal to the number of channels in this cellHTS object (dim(Data(cellHTSlist[["normalized"]]))[3]). Otherwise, the length of these vectors should be equal to the number of channels in the unpreprocessed cellHTS object (i.e., dim(Data(cellHTSlist[["raw"]]))[3]).
如果cellHTS对象，其中包含规范化的数据作为参数提供norm，posControls和negControls应该是渠道的数量等于在此cellHTS的长度对象（dim(Data(cellHTSlist[["normalized"]]))[3]）。否则，这些向量的长度应该是平等的通道数量unpreprocessedcellHTS对象（即dim(Data(cellHTSlist[["raw"]]))[3]）。
By default, if posControls is not given, "pos" will be taken as the name for the wells containing positive controls. Similarly, if negControls is missing, by default "neg" will be considered as the name used to annotate the negative controls. The content of posControls and negControls will be passed to regexpr for pattern matching within the well annotation given in column controlStatus of the featureData slot of the cellHTS object. If no controls are available for a given channel, use "" or NA for that channel. For example, posControls = c("", "(?i)^diap$") means that channel 1 has no positive controls, while "diap" is the positive control for channel 2.
默认情况下，如果posControls没有给出，“POS”将被视为包含阳性对照井的名字。同样，如果negControls缺少，默认情况下，“南德”将被视为阴性对照用来注释的名称。 posControls和negControls将传递给regexpr以及注释内的匹配模式在列给controlStatusfeatureData插槽的<内容X>对象。如果没有控制对于一个给定的通道，该通道使用cellHTS或""。例如，NA1通道意味着没有阳性对照，而“diap”通道2的阳性对照。
The arguments posControls and negControls are particularly useful in multi-channel data since the controls might be reporter-specific, or after normalizing multi-channel data.
论据posControls和negControls是特别有用的，因为在多通道数据的控制可能是特定的记者，或标准化后多通道数据。
In the case of a two-way assay, where two types of "positive" controls are used in the screen ("activators" and "inhibitors"), posControls should be defined as a list with two components (called act and inh), each of which should be vectors of regular expressions of the same length as the current number of reporters (as explained above).
在双向检测，在屏幕上使用两种类型的“积极”的控制（“激活”和“抑制剂”），posControls应作为一个列表定义有两个组件的情况下（称为act和inh），其中每一个应该作为当前的记者人数（如上所述）的相同长度的正则表达式的向量。
By default, tooltips doing the mapping between the probe annotation and the plate wells are not added to the plate plots and to the overall screen plot. If any of the cellHTS objects in cellHTSlist is annotated, the probe annotation uses the information contained either in column GeneSymbol or column GeneID (if the former is missing) of the featureData slot of the annotated cellHTS object. Otherwise, the mapping simply uses the well
默认情况下，提示做探针注释和板井之间的映射不会加入到板图和整体画面图。如果有任何的cellHTS对象cellHTSlist注释，探针注释使用GeneSymbol或列列GeneID（如果前丢失）所载的资料featureData插槽注明cellHTS对象。否则，映射只需使用以及
值----------Value----------
The function is called for its side-effect. It returns a character with the full path and name of the report index file, this is an HTML file which can be read by a web browser.
该功能被称为其副作用。它返回一个字符，报告索引文件的完整路径和名称，这是一个HTML文件，可以通过网页浏览器读取。
作者（S）----------Author(s)----------
Florian Hahne <a href="mailto:florian.hahne@novartis.com">florian.hahne@novartis.com</a>, Ligia P. Bras
<a href="mailto:ligia@ebi.ac.uk">ligia@ebi.ac.uk</a>, Wolfgang Huber <a href="mailto:huber@ebi.ac.uk">huber@ebi.ac.uk</a>,
Gabor Bakos
参考文献----------References----------
screens, Genome Biology 7, R66.
参见----------See Also----------
plotPlate,
plotPlate
举例----------Examples----------
data(KcViabSmall)
pCtrls <- c("pos")
nCtrls <- c("neg")
## Not run: [＃无法运行：]
## or for safety reasons (not a problem for the current well annotation, however) [＃或出于安全的原因（不是问题，但是当前以及注解）]
pCtrls <- c("^pos$")
nCtrls <- c("^neg$")
writeReport(raw=KcViabSmall, posControls=pCtrls, negControls=nCtrls)
## same as [＃一样]
## writeReport(raw=KcViabSmall)[＃writeReport（原始KcViabSmall）]
xn <- normalizePlates(KcViabSmall, scale="multiplicative", log=FALSE, method="median")
xsc <- scoreReplicates(xn, sign="-", method="zscore")
xsc <- summarizeReplicates(xsc, summary="min")
## to turn on the tooltips in the plate plots and in the image screen plot:[＃开启工具提示在板图和影像画面的图：]
writeReport(raw=KcViabSmall, normalized=xn, scored=xsc, force=TRUE, map=TRUE, plotPlateArgs = TRUE, imageScreenArgs=list(zrange=c(-4,4)))
## End(Not run)[＃结束（不运行）]
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 2012-2-25 14:19:44
