MAplotPara(affyPara)
MAplotPara()所属R语言包：affyPara
Parallelized relative M vs. A plots for Microarray Data
并行相对与微阵列数据的一个图中号
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Parallelized creation of M vs A plots. Where M is determined relative to a specified chip or to a pseudo-median reference chip. And optimized plots for a large number of microarrays.
并行创建的M VS的图。其中M是相对确定到指定的芯片或伪中位数参考芯片。大量的芯片和优化的图。
用法----------Usage----------
MAplotPara(object,
log=TRUE,
type=c("both","pm","mm"),
ref=NULL,
which=NULL,
ref.title="vs mean ref.Array",
subset=NULL,
span=1/4,
show.statistics=TRUE,
family.loess ="gaussian",
pch=".",
plot =TRUE,
cutoff =0.5,# add parameter to generic function ma.plot
level=1,
cluster, verbose = getOption("verbose"),
... )
参数----------Arguments----------
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：...
Additional parameters for the routine.
例行的附加参数。
参数：log
A logical value. TRUE as default. Computes logarithms of Array's intensities.
一个逻辑值。默认为true。计算数组的强度的对数。
参数：type
Defines how the Affimetrix Array's intensities should be considered (only for Affymetrix: perfect match(pm), mismatch or both).
定义应考虑如何Affimetrix阵列的强度（仅适用于Affymetrix公司：完美的比赛（下午），不匹配或两者）。
参数：ref
gives the possibility to define some array of the Affybatch object as 'medianchip' otherwise it will be calculate as reference median array.
给人的可能性定义为“medianchip一些的Affybatch对象数组，否则将被计算作为参考中位数阵列。
参数：which
A list of index samples from the object class, which indicates the samples to be ploted.
从对象类的名单，这表明样品ploted指数样本。
参数：ref.title
character- gives a 'title' to label the plots by ma.plot function.
字符给出了一个“标题”标签ma.plot功能图。
参数：subset
A set of indices to use when drawing the loess curve.
黄土曲线绘制时使用的一套指数。
参数：span
span to be used for loess fit.
跨度黄土适合使用。
参数：family.loess
"guassian" or "symmetric" as in loess.
"guassian"或"symmetric"黄土。
参数：show.statistics
A logical value. TRUE as default. If true some summary statistics of the M values are drawn.
一个逻辑值。默认为true。如果真M值的一些汇总统计得出的。
参数：pch
Graphical plotting 'character'. Default Value "." equivalently to pch = 46 from the function points
图形绘制字“。默认值"."等价pch = 46从功能点
参数：plot
A logical value. TRUE as default, MAplots will be drawn otherwise only the "bad" quality arrays will be calculated.
一个逻辑值。默认为true，MAplots将绘制，否则将计算只有“坏”的质量方针阵列。
参数：cutoff
numerical between [0.0-1.0]. As default 0.5. It is considered as limit for the sigma parameter, which is one of the three classificators for the 'bad' quality arrays by MAplotsPara.
[0.0-1.0]之间的数值。由于默认0.5。它被认为是西格玛参数的限制，这是一个“坏”由MAplotsPara质量阵列的三个classificators。
参数：level
level- numerical - indicates which level of "bad" quality arrays should be plot if plotDraw =TRUE: 1 - only first level "bad" quality will be considered. First level "bad" array quality are the arrays considered as "bad" after the three possible parameter: S, loess, and sigma 2 - first level "bad" quality and second level will be considered. Second level "bad" quality Arrays are the arrays which has been classified as bad after two of the three possible parameter 3 - all levels will be plot : first, second and third. Third level "bad" quality Arrays are the arrays which are considered as "bad" after one of the three parameter.
级数值 - 表示“坏”的质量方针阵列级别应该图如果plotDraw = TRUE：1 - 只有第一级的“坏”的质量方针，将予以考虑。第一级的“坏”的数组质量阵列后认为“坏”的三个可能的参数：S，黄土，和sigma 2 - 第一级的“坏”的质量方针，将被视为第二个层次。第二个层次的“坏”质量阵列阵列已被归类为坏后两三个可能的参数3 - 各级图：第一，第二和第三。第三个层次的“坏”质量阵列阵列认为是“坏”后的三个参数之一。
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----------
MAplotPara is a function based on the generic function ma.plot from affy package. Only the following parameters are original for MAplotPAra: cluster, object, cuttof, plot, level The parameter ref.fn=c("median","mean") is not allowed because it is not possible to calculate the reference median array as parallelized.
MAplotPara是一个功能包从affy通用功能ma.plot的基础上。只有以下参数是原始MAplotPAra：聚类，对象，cuttof，图，水平参数ref.fn = C（“中间”，“指”）是不允许的，因为它是无法计算的参考中位数阵列作为并行。
MAplotPara is the parallelized function for MA plots of probe intensities. It is a function to check and control the Data quality of the samples using the MA plot method. For serial function an more details see boxplot. This function is optimized for huge numbers of microarray data.
MAplotPara探针强度的主图的并行功能。这是一个使用主图方法的样本数据质量检查和控制功能。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。
值----------Value----------
MAplotPara return a list with four elements: values_MAP, loess_y, quality_MAP, results_MAP.
MAplotPara返回与四个要素：values_MAP，loess_y，quality_MAP，results_MAP。
参数：values_MAP
is a matrix which contains the calculated values for all arrays of the object (sampleNames, S, osc_Loess, sigma, var_sigma).
是一个矩阵，其中包含对象的所有阵列的计算值（sampleNames，S，osc_Loess，sigma，var_sigma）。
参数：loess_y
contains the y values (50 points) of the loess curve, which are used to calculate the osc_Loess from values_MAP
包含的黄土曲线y值（50分），这是用来计算从osc_Loessvalues_MAP
参数：quality_MAP
list which contains all "bad" quality Arrays
列表，其中包含所有的“坏”的质量阵列
参数：results_MAP
summary from quality_MAP 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quality_MAP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。如果数组是不是在这个水平，1，如果它被视为“坏”的样本归类在这个级别，可能值是0。
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)
##MA of Dilution data (affybatch)[＃马（affybatch）的稀释数据]
ma1 <- MAplotPara(Dilution)
## MAplot to a pdf file[＃MAplot为PDF文件]
pdf(file="maplot.pdf", title="AffyBatch MAplot")
ma2 <- MAplotPara(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。
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 11:18:25
