summarize(beadarray)
summarize()所属R语言包：beadarray
Create a summarized object
创建一个总结对象
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Function to summarize the data in a beadLevelData object into a form more ameanable for downstream analysis (with the same number of observations for each bead type).
函数beadLevelData对象的数据总结成一种更适合下游分析（每个珠类型相同数量的意见）ameanable。
用法----------Usage----------
summarize(BLData, channelList = list(greenChannel), probeIDs=NULL, useSampleFac = FALSE, sampleFac= NULL, weightNames = "wts", removeUnMappedProbes = TRUE)
参数----------Arguments----------
参数：BLData
An object of class beadLevelData
一个类beadLevelData的对象
参数：channelList
List of objects of class illuminaChannel that defines the summarisation to be performed. The default is to do a log2 transformation and report the mean and standard deviation of each bead type after outlier removal.
类的illuminaChannel定义进行summarisation的对象名单。默认是做的log2改造和报告的均值和标准差，每个类型后离群去除珠。
参数：probeIDs
Vector of ArrayAddressIDs to be included in the summarized object. The default is to summarize all probes.
被列入ArrayAddressIDs矢量在总结对象。默认是总结所有探针。
参数：useSampleFac
if TRUE sections belonging to the same biological sample will be combined. The default is to summarize each section separately.
如果属于同一生物样品的真实部分将被合并。默认是每个部分分别总结。
参数：sampleFac
optional character vector giving which a sample identifer for each section
可选特征向量，其中每个部分样品标识符
参数：weightNames
name of column in the beadLevelData to take extract weights
列的名字在beadLevelData采取提取物重量
参数：removeUnMappedProbes
if TRUE and annotation information is stored in the beadLevelData object, any ArrayAddressIDs that cannot be mapped to ILMN IDs will be removed.
如果真实和注释信息被储存在beadLevelData对象，任何不能映射到ILMN标识ArrayAddressIDs将被删除。
Details
详情----------Details----------
From beadarray version 2.0 onwards, users are allowed more flexibility in how to create summarized data from bead-level data. The illuminaChannel is a means of allowing this flexibility by definining how summarization will be performed on each array section in the bead-level data object. The three keys steps applied to each section are; 1) use a transform function to get the quantities to be summarized (one value per bead). The most common use-case would be to extract the Green channel intensities and possibly perform a log2 transformation. 2) remove any outliers from this list of values 3) split the values according to ArrayAddressIDs and apply the definied exprFun and varFun to the quantities belonging to each ArrayAddress.
从beadarray版本2.0起，允许用户更灵活地在如何创建从珠层次的数据汇总的数据的。 “illuminaChannel是允许的划总结如何将每个阵列节在珠级别的数据对象，这种灵活性的一种手段。的三把钥匙适用于每节的步骤是：1）使用转换函数来获得概括的数量（每一个珠值）。最常见的使用情况，将提取的绿色通道强度和可能执行的log2改造。 2）删除任何离群从这个列表值3）分裂值根据ArrayAddressIDs，申请的definiedexprFun和varFun属于每个ArrayAddress数量。
Some Illumina chips have multiple sections for the same biological sample; for example the HumanWG-6 chip or the Infinium genotyping chips. For such cases it may be more convenient to produce a summarized object where each column in the output is a different biological sample. This is especially important for genotpying chips where different SNPs are interrogated on the different sections, making a section-based summary problematic.
一些Illumina的芯片具有相同的生物样品的多个部分;例如的HumanWG-6芯片或Infinium基因分型芯片。对于这样的情况下，它可能是更方便地产生一个概括的对象，在输出的每一列是一个不同的生物样品。这是特别重要的genotpying不同的单核苷酸多态性的不同部分审讯芯片，使得基于一节总结的问题。
If the useSampleFac argument is set to TRUE, beadarray will try and combine sections belonging to the same sample. If the location of the sdf file for the chip is sucessfully stored in the experimentData slot of the beadLevelData object, the sdf will be interrogated to determine how samples were allocated to the chip. Otherwise the user can specifiy a sample factor that is the same length as the number of sections. If the sample factor is not supplied, or cannot be determined, then beadarray will summarize each section separately.
如果useSampleFac参数设置为TRUE，beadarray会会尝试，并结合部分属于同一样品。如果成功地在experimentDatabeadLevelData对象插槽存储芯片sdf文件的位置，自卫队将被审问，以确定如何样品被分配到芯片。否则，用户可以说明指样本的因素是相同长度的节数。如果样品的因素是不提供的，或不能确定，然后beadarray将总结每个部分分开。
During the course of the summary, ArrayAddressIDs present in the beadLevelData object will be converted to Illumina IDs (prefix ILMN) if the annotation of the object was set by readIllumina or setAnnotation. The rownames of the resulting ExpressionSetIllumina will be set to these new IDs, and the featureData slot will contain the original and new IDs. Any control probes present in the beadLevelData object will retain their original ArrayAddressID and the Status vector in featureData will report if each probe is a control or regular probe. Some ArrayAddressIDs present in the beadLevelData object may be neither regular probes will ILMN IDs, or control probes. These are internal controls used by Illumina and can be stopped from appearing in the summarized object by choosing the removeUnmappedProbes = TRUE option.
在总结的过程中，ArrayAddressIDs中存在的beadLevelData对象将被转换为Illumina公司的ID（前缀ILMN）如果对象的注释readIllumina或setAnnotation。设置，造成ExpressionSetIllumina rownames将到这些新的ID，和featureData插槽将包含原有的和新的ID。目前beadLevelData对象将任何控制探针保留其原有的ArrayAddressIDfeatureData报告，如果每个探针是一种控制或定期探针和状态向量。一些ArrayAddressIDs提出beadLevelData对象可能既不定期探测器将ILMN ID或控制探针。这些都是用于Illumina公司的内部控制，并可以从停止出现在总结对象的选择removeUnmappedProbes = TRUE选项。
The user can specify a vector of ArrayAddressIDs to be summarized using the probeIDs argument. Otherwise, a unique set of IDs is derived from all the array sections in the beadLevelData object.
用户可以指定使用probeIDs参数的向量概括ArrayAddressIDs，。否则，一套独特的ID来自所有beadLevelData对象的数组部分。
值----------Value----------
Returns an object of class ExpressionSetIllumina
返回类ExpressionSetIllumina的对象
作者（S）----------Author(s)----------
Mark Dunning
举例----------Examples----------
if(require(beadarrayExampleData)){
data(exampleBLData)
bsd = summarize(exampleBLData)
myMean = function(x) mean(x,na.rm=TRUE)
mySd = function(x) sd(x,na.rm=TRUE)
greenChannel = new("illuminaChannel", logGreenChannelTransform, illuminaOutlierMethod, myMean, mySd,"G")
bsd = summarize(exampleBLData, channelList = list(greenChannel))
bsd
}
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 13:06:44
