boxplotPara(affyPara)
boxplotPara()所属R语言包：affyPara
Parallelized Box Plots for Microarray Data
微阵列数据的并行箱线图
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Parallelized functions for Box Plots for Microarray Data. And optimized plots for a large number of microarrays.
并行微阵列数据的箱线图的功能。大量的芯片和优化的图。
用法----------Usage----------
boxplotPara(object,
nSample=if(length(object)> 200) nSample<-200 else nSample <- length(object),
iqrMethod=TRUE, percent=0.05,
typDef="mean", plot=TRUE,
plotAllBoxes=TRUE,
cluster, verbose = getOption("verbose"))
参数----------Arguments----------
参数：nSample
A numeric value. Indicates the number of maximal samples that should be plot at the same boxplot. default: 250
一个数值。表示，应该在同一盒形图的积最大的样本数。默认值：250
参数：iqrMethod
A logical value, if TRUE the second method will be considered to calculate the "bad" quality Samples otherwise the first Method. See Details. default: TRUE
一个逻辑值，如果为true，第二个方法，第一种方法计算“坏”的质量样品，否则将被视为。查看详细信息。默认：true
参数：percent
A numeric value [0.0-1.1]. If iqrMethod=TRUE the second method will be considered to calculate the "bad" quality Samples otherwise the first Method. default: 0.05
数值[0.0-1.1]。第二种方法如果iqrMethod = TRUE，第一种方法计算“坏”的质量样品，否则将被视为。默认值：0.05
参数：typDef
A character value. Indicates how the default Sample should be calculated. As median or mean from all Samples value. Only three possibilities: "media", "mean", c("median", "mean"). default: "mean"
一个字符值。表示默认的样品应如何计算。从所有样本值中位数或平均。只有三种可能性：“媒介”，“中庸”，C（“中位数”，“中庸”）。默认：“是什么意思”
参数：plot
A logical value. Indicates if graphics should be drawn. default: TRUE
一个逻辑值。指示是否应绘制图形。默认：true
参数：plotAllBoxes
A logical value. If TRUE then all Samples will be ploted, if FALSE only bad arrays will be plotted. default: TRUE
一个逻辑值。如果是TRUE，则所有样品将ploted，如果为FALSE唯一不好的阵列将被绘制。默认：true
参数：object
An object of class AffyBatch OR a character vector with the names of CEL files OR a (partitioned) list of character vectors with CEL file names.
对象类AffyBatch或CEL文件的名称或一个characterCEL文件名向量（分区）列表character向量。
参数：cluster
A cluster object obtained from the function makeCluster in the SNOW package. For default .affyParaInternalEnv$cl will be used.
在雪包的功能makeCluster获得聚类对象。 默认.affyParaInternalEnv$cl将使用。
参数：verbose
A logical value. If TRUE it writes out some messages. default: getOption("verbose")
一个逻辑值。如果TRUE写了一些消息。默认：getOption（“冗长”）
Details
详情----------Details----------
boxplotPara is the parallelized function for box plots of probe intensities. It is a function to check and control the Data quality of the samples using the boxplot methode. For serial function an more details see boxplot. This function is optimized for huge numbers of microarray data.
boxplotPara是探针强度的箱线图的并行功能。它是一个函数来检查和数据质量控制样品使用的盒形图逼近法。对于串行功能的更多细节见盒形图。此功能进行了优化，大量的芯片数据。
For using this function a computer cluster using the SNOW package has to be started. Starting the cluster with the command makeCluster generates an cluster object in the affyPara environment (.affyParaInternalEnv) and no cluster object in the global environment. The cluster object in the affyPara environment will be used as default cluster object, therefore no more cluster object handling is required. The makeXXXcluster functions from the package SNOW can be used to create an cluster object in the global environment and to use it for the preprocessing functions.
要开始使用此功能的计算机聚类使用雪包。启动命令makeCluster聚类产生的affyPara环境（。affyParaInternalEnv）的，并没有在全球环境中的聚类对象的聚类对象。默认聚类对象将被用作聚类对象在affyPara环境，因此没有更多的聚类对象的处理需要。 makeXXXcluster从包雪功能，可用于创建一个在全球环境中的聚类对象和使用它的预处理功能。
We need to calculate a default Sample as reference , which has been built from all Samples data. Therefore the first is the calculation of the boxplot.stats, it will be made parallel at the cluster. The calculated values are merged at the master as well as the following calculations, plots and histograms There are two possibility to calculate the limits between the "good-bad" quality Samples: 1. From the differences between defaultSample values (only media, HL nad HU will be considered) and all the samples. At limit will be considered as critical and it help to calculate the "bad" quality Samples. (it is fixed as parameter and thus do it not so sure) 2. From the median and IQR obtained from a boxplot, which is calculated from all Samples values. The outliers of these boxplot are the "bad" quality Samples. It should be as default parameter.
我们需要计算作为参考，它已经从所有样本数据建立一个默认的样本。因此，首先是计算的boxplot.stats，将并行聚类。主以及以下计算合并计算值，图和直方图有两种可能性计算“好不好”的质量样品之间的界限：1。从defaultSample值（仅媒体，将被视为HL河畔胡）和所有样品之间的差异。在限制将被视为关键，它有助于计算“坏”的质量样品。 （固定为参数，从而做到这一点不那么肯定）2。从一个盒形图，这是从所有样本值计算所得的中位数和四分。这些盒形图的离群是“坏”的质量样品。它应该是默认参数。
值----------Value----------
boxplotPara returns a list with elements from the boxplot.stats function ('stats', 'n', 'conf', 'out', 'group', 'names') and QualityPS, values_boxP and results_boxP.
boxplotPara返回的boxplot.stats功能（统计，N，conf的，出，组，名）和QualityPS，values_boxP的元素列表results_boxP。
参数：qualityPS
is a list which contains all "bad" quality Arrays classified in levels.
是一个列表，其中包含所有的“坏”的质量水平分类的数组。
参数：values_boxP
contains the calculated differences and limits, which are used to make the classification of the Arrays in levels.
包含计算的差异和限制，这是用来使各级阵列分类。
参数：results_boxP
summary from qualityPS as matrix, which contains only the Arrays that are considered as "bad" quality and in which levels are they classified. Possible values are 0 if the Array is not at this levels and 1 if it is classified as "bad" sample at this level
汇总qualityPS为基体，其中只包含被视为“坏”的质量方针，并在这水平，他们归类阵列。可能值是0，如果数组是不是在这个水平，1，如果它在这个级别作为“坏”的样本分类
作者（S）----------Author(s)----------
Esmeralda Vicedo <e.vicedo@gmx.net>, Markus Schmidberger <a href="mailto:schmidb@ibe.med.uni-muenchen.de">schmidb@ibe.med.uni-muenchen.de</a>, Ulrich Mansmann <a href="mailto:mansmann@ibe.med.uni-muenchen.de">mansmann@ibe.med.uni-muenchen.de</a>
举例----------Examples----------
## Not run: [＃无法运行：]
library(affyPara)
if (require(affydata)) {
data(Dilution)
makeCluster(3)
##boxplot of Dulution data (affybatch) [＃盒形图（affybatch）的Dulution数据]
box1 <- boxplotPara(Dilution)
## boxplots to a pdf file[＃盒状图的PDF文件]
pdf(file="boxplot.pdf", title="AffyBatch Boxplot")
box2 <- boxplotPara(Dilution)
dev.off()
stopCluster()
}
## 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。
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发表于 2012-2-25 11:17:46
