compensation-class(flowCore)
compensation-class()所属R语言包：flowCore
Class "compensation"
类“补偿”
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Class and methods to compensate for spillover between channels by applying a spillover matrix to a flowSet or a flowFrame assuming a simple linear combination of values.
类和方法来补偿通道间的外溢应用外溢矩阵flowSet或flowFrame假设一个简单值的线性组合。
用法----------Usage----------
compensation(..., spillover,
compensationId="defaultCompensation")
compensate(x, spillover, ...)
参数----------Arguments----------
参数：spillover
The spillover or compensation matrix.
外溢或补偿矩阵。
参数：compensationId
The identifier for the compensation object.
为补偿对象的标识符。
参数：x
An object of class flowFrame or flowSet.
一个对象类flowFrame或flowSet。
参数：...
Further arguments. The constructor is designed to be useful in both programmatic and interactive settings, and ... serves as a container for possible arguments. The following combinations of values are allowed: Elements in ... are character scalars of parameter names or transform objects and the colnames in spillover match to these parameter names. The first element in ... is a character vector of parameter names or a list of character scalars or transform objects and the colnames in spillover match to these parameter names. Argument spillover is missing and the first element in ... is a matrix, in which case it is assumed to be the spillover matrix. ... is missing, in which case all parameter names are taken from the colnames of spillover.
进一步的论据。构造设计是有用的方案和互动设置，...作为一个可能的参数的容器。允许下列值的组合：在元素... character参数名称或transform对象和在colnames的标量spillover匹配这些参数的名称。在第一元素...是一个向量参数名称或了character标量或character对象，并在colnames的名单transformspillover匹配这些参数的名称。 spillover参数缺少的第一个元素... matrix，在这种情况下，它被认为是溢出矩阵。 ...丢失，都是从spillover的colnames采取在这种情况下，所有参数名。
Details
详情----------Details----------
The essential premise of compensation is that some fluorochromes may register signals in detectors that do not correspond to their primary detector (usually a photomultiplier tube). To compensate for this fact, some sort of standard is used to obtain the background signal (no dye) and the amount of signal on secondary channels for each fluorochrome relative to the signal on their primary channel.
补偿的基本前提，是可以注册一些荧光信号探测器，不符合他们的主要探测器（通常是一个光电倍增管）。为了弥补这一事实，被用来获取某种标准的背景信号（无染料）每个荧光相对次要渠道，他们的主要通道上的信号量和信号。
To calculate the spillover percentage we use either the mean or the median (more often the latter) of the secondary signal minus the background signal for each dye to obtain n by n matrix, S, of so-called spillover values, expressed as a percentage of the primary channel. The observed values are then considered to be a linear combination of the true fluorescence and the spillover from each other channel so we can obtain the true values by simply multiplying by the inverse of the spillover matrix.
计算外溢的百分比，我们使用每个染料的均值或中位数的辅助信号（后者更经常）减去背景信号获得n矩阵n，S所谓的溢出值，作为主渠道的百分比表示。观测值，然后考虑是一个真正的荧光和溢出从对方通道的线性组合，所以我们可以通过简单由外溢矩阵的逆乘以获得真正的价值。
The spillover matrix can be obtained through several means. Some flow cytometers provide a spillover matrix calculated during acquisition, possibly by the operator, that is made available in the metadata of the flowFrame. While there is a theoretical standard keyword \$SPILL it can also be found in the SPILLOVER or SPILL keyword depending on the cytometry. More commonly the spillover matrix is calculated using a series of compensation cells or beads collected before the experiment. If you have set of FCS files with one file per fluorochrome as well as an unstained FCS file you can use the spillover method for flowSets to automatically calculate a spillover matrix.
溢出矩阵可以通过以下几种方式获得。一些流式单元仪提供了一个的外溢矩阵在收购过程中，可能是由运营商，是提供中的flowFrame的元数据计算。虽然是一个理论上的标准关键字\$SPILL它也可以被发现在SPILLOVER或SPILL关键字视仪。更常用的外溢矩阵计算使用了一系列补偿单元或实验前收集的珠子。的FCS文件设置一个文件每荧光以及未染色的FCS文件如果你已经可以使用spilloverflowSets方法，自动计算出溢出矩阵。
The compensation class is essentially a wrapper around a matrix that allows for transformed parameters and method dispatch.
基本上是compensation类，允许转换参数和方法调度matrix周围的包装。
值----------Value----------
A compensation object for the constructor.
一个compensation对象的构造。
A flowFrame or flowSet for the compensate methods.
一个flowFrame或flowSetcompensate方法。
类的对象----------Objects from the Class----------
Objects should be created using the constructor compensation(). See the Usage and Arguments sections for details.
应该创建对象使用构造compensation()。见Usage和Arguments详情路段。
插槽----------Slots----------
spillover: Object of class matrix; the
spillover：对象类matrix;
compensationId: Object of class character. An
compensationId类character的对象。一个
parameters: Object of class parameters. The flow parameters for which the compensation is defined. This can also be objects of class transform, in which
parameters类parameters的对象。赔偿被定义为流动参数。这也可能是类transform的对象，在其中
方法----------Methods----------
compensate signature(x = "flowFrame", spillover = "compensation"): Apply the compensation defined in a compensation object on a flowFrame. This returns a compensated flowFrame.
补偿signature(x = "flowFrame", spillover = "compensation")：申请compensationflowFrame对象上定义的补偿。这将返回一个补偿flowFrame。
Usage:
用法：
compensate(flowFrame, compensation)
compensate(flowFrame, compensation)
compensate signature(x = "flowFrame", spillover = "matrix"): Apply a compensation matrix to a flowFrame. This returns a compensated flowFrame.
补偿signature(x = "flowFrame", spillover = "matrix")：申请一个补偿矩阵flowFrame。这将返回一个补偿flowFrame。
Usage:
用法：
compensate(flowFrame, matrix)
compensate(flowFrame, matrix)
compensate signature(x = "flowFrame", spillover = "data.frame"):Try to coerce the data.frame to a matrix and apply that to a flowFrame. This returns a compensated flowFrame.
补偿signature(x = "flowFrame", spillover = "data.frame")：尝试一个data.frame和应用强迫matrix，到flowFrame。这将返回一个补偿flowFrame。
Usage:
用法：
compensate(flowFrame, data.frame)
compensate(flowFrame, data.frame)
identifier, identifier<- signature(object = "compensation"): Accessor and replacement methods for the compensationId slot.
标识符，标识符< - signature(object = "compensation")：compensationId插槽存取和更换方法。
Usage:
用法：
identifier(compensation)
identifier(compensation)
identifier(compensation) <- value
identifier(compensation) <- value
parameters signature(object = "compensation"): Get the parameter names of the compensation object. This method also tries to resolve all transforms and transformReferences before returning the parameters as character vectors. Unresolvable references return NA.
参数signature(object = "compensation")：获取compensation对象的参数名称。这种方法也试图解决所有的transforms和transformReferences，然后返回的参数作为特征向量。不能解决的引用返回NA。
Usage:
用法：
parameters(compensation)
parameters(compensation)
show signature(object = "compensation"): Print details about the object.
显示signature(object = "compensation")：关于对象的打印细节。
Usage:
用法：
This method is automatically called when the object is printed on the screen.
这种方法被自动调用对象时在屏幕上打印。
作者（S）----------Author(s)----------
F.Hahne, B. Ellis, N. Le Meur
参见----------See Also----------
spillover
spillover
举例----------Examples----------
## Read sample data and a sample spillover matrix[＃读取样本数据和样品溢出矩阵]
samp <- read.flowSet(path=system.file("extdata", "compdata", "data",
package="flowCore"))
cfile <- system.file("extdata","compdata","compmatrix", package="flowCore")
comp.mat <- read.table(cfile, header=TRUE, skip=2, check.names = FALSE)
comp.mat
## compensate using the spillover matrix directly[＃使用直接外溢矩阵，补偿]
summary(samp)
samp <- compensate(samp, comp.mat)
summary(samp)
## create a compensation object and compensate using that[＃创建一个补偿对象和补偿使用，]
comp <- compensation(comp.mat)
compensate(samp, comp)
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 17:40:53
