flowFrame-class(flowCore)
flowFrame-class()所属R语言包：flowCore
'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run
“flowFrame：一类用于存储从流式单元仪观察单元人口定量属性运行
译者：生物统计家园网 机器人LoveR
描述----------Description----------
This class represents the data contained in a <acronym>FCS</acronym> file or similar data structure. There are three parts of the data:
这个类代表在<acronym>中包含的数据FCS</首字母缩写>文件或类似的数据结构。有三个部分数据：
a numeric matrix of the raw measurement values with <KBD>rows=events</KBD> and <KBD>columns=parameters</KBD>
数字矩阵的原始测量值与<KBD>行=事件</大骨节病和<KBD>列=参数</大骨节病>
annotation for the parameters (e.g., the measurement channels, stains, dynamic range)
参数的注释（例如，测量通道，污渍，动态范围）
additional annotation provided through keywords in the <acronym>FCS</acronym> file
通过关键字在<acronym>FCS</首字母缩写>文件提供额外的注释
Details
详情----------Details----------
Objects of class flowFrame can be used to hold arbitrary data of cell populations, acquired in flow-cytometry.
flowFrame类的对象，可以用来举行的单元群，流式单元仪获得任意数据。
<acronym>FCS</acronym> is the Data File Standard for Flow Cytometry, the current version is FCS 3.0. See the vignette of this package for additional information on using the object system for handling of flow-cytometry data.
<acronym>FCS> </首字母缩写，是流式单元仪数据文件的标准，目前的版本是3.0的FCS。看到这个包使用流式单元仪数据处理系统对象的附加信息的小插曲。
创建对象----------Creating Objects----------
Objects can be created using<br> new("flowFrame",<br> exprs = ...., Object of class matrix<br> parameters = ...., Object of class AnnotatedDataFrame<br> description = ...., Object of class list<br> )<br>
可以创建对象使用参考 new("flowFrame",参考 exprs = ...., Object of class matrix参考 parameters = ...., Object of class AnnotatedDataFrame参考 description = ...., Object of class list参考 )参考
or the constructor flowFrame, with mandatory arguments exprs and optional arguments parameters and description.
或构造flowFrame，强制性的参数exprs参数和可选参数parameters和description。
flowFrame(exprs, parameters, description=list())
flowFrame(exprs, parameters, description=list())
To create a flowFrame directly from an <acronym>FCS</acronym> file, use function read.FCS. This is the recommended and safest way of object creation, since read.FCS will perform basic data quality checks upon import. Unless you know exactly what you are doing, creating objects using new or the constructor is discouraged.
要创建一个flowFrame直接从<acronym>FCS</首字母缩写>文件，使用功能read.FCS。这是创建对象的建议和最安全的方式，read.FCS自将执行基本数据后，进口的质量检查。除非你知道你正在做什么，创建对象使用new或气馁的构造。
插槽----------Slots----------
exprs: Object of class matrix containing the measured intensities. Rows correspond to cells, columns to the different measurement channels. The colnames attribute of the matrix is supposed to hold the names or identifiers for the channels. The rownames attribute would usually not be set.
exprs类matrix包含测量强度的对象。行对应的单元，列不同的测量通道。 colnames矩阵的属性应该保持通道的名称或标识符。 rownames属性一般不会被设置。
parameters: An AnnotatedDataFrame containing information about each column of the flowFrame. This will generally be filled in by read.FCS or similar functions using data from the
parameters：AnnotatedDataFrame约每个flowFrame列含有信息。这一般会被填补read.FCS或类似使用的数据的功能
description: A list containing the meta data included
description：一个列表，其中包含的元数据包括
方法----------Methods----------
There are separate documentation pages for most of the methods listed here which should be consulted for more details.
有单独的文档页面，这里列出的方法应咨询更多详情。
[ Subsetting. Returns an object of class flowFrame. The subsetting is applied to the exprs slot, while the description slot is unchanged. The syntax for subsetting is similar to that of data.frames. In addition to the usual index vectors (integer and logical by position, character by parameter names), flowFrames can be subset via filterResult and filter objects.
[子集。类flowFrame返回一个对象。该子集被应用到exprs插槽，而description插槽是不变的。语法子集是类似data.frames。除了通常的指数矢量（整数和逻辑位置，参数名称的字符），flowFrames可以通过filterResult和filter对象的子集。
Usage:
用法：
flowFrame[i,j]
flowFrame[i,j]
flowFrame[filter,]
flowFrame[filter,]
flowFrame[filterResult,]
flowFrame[filterResult,]
Note that the value of argument drop is ignored when subsetting flowFrames.
请注意，值的参数drop子集时，会忽略flowFrames。
\$ Subsetting by channel name. This is similar to subsetting of columns of data.frames, i.e., frame$FSC.H is equivalent to frame[, "FSC.H"]. Note that column names may have to be quoted if they are no valid R symbols (e.g. frame$"FSC-H").
\ $子集频道名称。这是类似的data.frames，即列的子集，frame$FSC.H相当于frame[, "FSC.H"]的。请注意，列名可能要报价，如果他们没有有效ŕ符号（例如frame$"FSC-H"）。
exprs, exprs<- Extract or replace the raw data intensities. The replacement value must be a numeric matrix with colnames matching the parameter definitions. Implicit subsetting is allowed (i.e. less columns in the replacement value compared to the original flowFrame, but all have to be defined there).
exprs，exprs < - 提取或替换原始数据的强度。替换值必须是匹配的参数定义的colnames数字矩阵。允许隐子集（即替换值少的列比原flowFrame，但都没有被定义）。
Usage:
用法：
exprs(flowFrame)
exprs(flowFrame)
exprs(flowFrame) <- value
exprs(flowFrame) <- value
head, tail Show first/last elements of the raw data matrix
头，尾，显示的原始数据矩阵中的第一个/最后一个元素
Usage:
用法：
head(flowFrame)
head(flowFrame)
tail(flowFrame)
tail(flowFrame)
description, description<- Extract or replace the whole list of annotation keywords. Usually one would only be interested in a subset of keywords, in which case the keyword method is more appropriate. The optional hideInternal parameter can be used to exclude internal FCS parameters starting with\$.
说明，描述< - 提取或替换整个列表的注释关键字。一般只会在关键字的一个子集感兴趣，在这种情况下，keyword方法是比较合适的。可选hideInternal参数可以用来排除内部的FCS参数与\$开始。
Usage:
用法：
description(flowFrame)
description(flowFrame)
description(flowFrame) <- value
description(flowFrame) <- value
keyword, keyword<- Extract ore replace one or more entries from the description slot by keyword. Methods are defined for character vectors (select a keyword by name), functions (select a keyword by evaluating a function on their content) and for lists (a combination of the above). See keyword for details.
关键字，关键字< - 提取矿石description关键字插槽更换一个或多个条目。方法被定义为特征向量（选择关键字的名字），功能（选择功能评估其内容中的关键字）和列表（以上的组合）。看到keyword详情。
Usage:
用法：
keyword(flowFrame)
keyword(flowFrame)
keyword(flowFrame, character)
keyword(flowFrame, character)
keyword(flowFrame, list)
keyword(flowFrame, list)
keyword(flowFrame) <- list(value)
keyword(flowFrame) <- list(value)
parameters, parameters<- Extract parameters and return an object of class AnnotatedDataFrame, or replace such an object. To access the actual parameter annotation, use pData(parameters(frame)). Replacement is only valid with AnnotatedDataFrames containing all varLabels name, desc, range, minRange and maxRange, and matching entries in the name column to the colnames of the exprs matrix. See parameters for more details.
参数，参数< - 提取参数并返回一个类的对象AnnotatedDataFrame，或更换这样一个对象。要访问的实际参数注解，使用pData(parameters(frame))。 AnnotatedDataFrames包含所有varLabels的name，desc，range，minRange和maxRange，<匹配条目，置换是唯一有效X>列name矩阵colnames的。看到exprs更多细节。
Usage:
用法：
parameters(flowFrame)
parameters(flowFrame)
parameters(flowFrame) <- value
parameters(flowFrame) <- value
Display details about the flowFrame object.
显示有关flowFrame对象。
summary Return descriptive statistical summary (min, max, mean and quantile) for each channel
摘要返回每个通道的描述性统计摘要（最小值，最大值，平均值和位数）
Usage:
用法：
summary(flowFrame)
summary(flowFrame)
plot Basic plots for flowFrame objects. If the object has only a single parameter this produces a histogram. For exactly two parameters we plot a bivariate density map (see smoothScatter and for more than two parameters we produce a simple splom plot. To select specific parameters from a flowFrame for plotting, either subset the object or specify the parameters as a character vector in the second argument to plot. The smooth parameters lets you toggle between density-type smoothScatter plots and regular scatterplots. For far more sophisticated plotting of flow cytometry data, see the flowViz package.
绘制基本图flowFrame对象。如果对象只有一个参数，这将产生一个histogram。整整两个参数，我们绘制二元密度图（见smoothScatter和两个以上的参数，我们产生了一个简单的splom图。要选择绘制的具体参数，从flowFrame，要么子集对象或指定的第二个参数作为特征向量参数plot。光滑参数，让您对于更为复杂的流式单元仪数据绘制密度型smoothScatter图和定期散点图之间切换。 ，看到flowViz包。
Usage:
用法：
plot(flowFrame, ...)
plot(flowFrame, ...)
plot(flowFrame, character, ...)
plot(flowFrame, character, ...)
plot(flowFrame, smooth=FALSE, ...)
plot(flowFrame, smooth=FALSE, ...)
ncol, nrow, dim Extract the dimensions of the data matrix.
NCOL，NROW，暗淡的数据矩阵中提取的尺寸。
Usage:
用法：
ncol(flowFrame)
ncol(flowFrame)
nrow(flowFrame)
nrow(flowFrame)
dim(flowFrame)
dim(flowFrame)
featureNames, colnames, colnames<- Extract parameter names (i.e., the colnames of the data matrix). colnames and featureNames are synonyms. For colnames there is also a replacement method. This will update the name column in the parameters slot as well.
featureNames，colnames，colnames < - 提取参数的名称（即数据矩阵colnames的）。 colnames和featureNames是同义词。 colnames还有一种替代方法。这将更新以及name插槽parameters在列。
Usage:
用法：
featureNames(flowFrame)
featureNames(flowFrame)
colnames(flowFrame)
colnames(flowFrame)
colnames(flowFrame) <- value
colnames(flowFrame) <- value
names Extract pretty formated names of the parameters including parameter descriptions.
漂亮的名字提取格式化的参数的名称，包括参数说明。
Usage:
用法：
names(flowFrame)
names(flowFrame)
identifier Extract GUID of a flowFrame. Returns the file name if no GUID is available. See identifier for details.
提取标识符GUIDflowFrame。如果没有GUID是可以返回的文件名。看到identifier详情。
Usage:
用法：
identifier(flowFrame)
identifier(flowFrame)
range Get dynamic range of the flowFame. Note that this is not necessarily the range of the actual data values, but the theoretical range of values the measurement instrument was able to capture. The values of the dynamic range will be transformed when using the transformation methods for flowFrames. Additional character arguments are evaluated as parameter names for which to return the dynamic range.
范围的flowFame获取的动态范围。请注意，这不一定是实际的数据值范围内，但理论值范围的测量仪器能够捕捉到。动态范围的值将被转化时使用flowFrames的变换方法。额外的字符参数被评为参数名称，返回的动态范围。
Usage:
用法：
range(flowFrame, ...)
range(flowFrame, ...)
each\_row, each\_col Apply functions over rows or columns of the data matrix. These are convenience methods. See each_col for details.
每个\ _row，每个\ _col应用了数据矩阵的行或列的功能。这些都是方便的方法。看到each_col详情。
Usage:
用法：
each_row(flowFrame, function, ...)
each_row(flowFrame, function, ...)
each_col(flowFrame, function, ...)
each_col(flowFrame, function, ...)
transform Apply a transformation function on a flowFrame object. This uses R's transform function by treating the flowFrame like a regular data.frame. flowCore provides an additional inline mechanism for transformations (see %on%) which is strictly more limited than the out-of-line transformation described here.
flowFrame对象转化应用转换功能。使用治疗像一个普通的transformflowFrameR的data.frame功能。 flowCore提供额外的内联机制的转换（见%on%），这是严格多行，这里描述的改造有限。
Usage:
用法：
transform(flowFrame, ...)
transform(flowFrame, ...)
filter Apply a filter object on a flowFrame object. This returns an object of class filterResult, which could then be used for subsetting of the data or to calculate summary statistics. See filter for details.
筛选申请filterflowFrame对象的对象。这将返回一个类filterResult，然后可以用于数据的子集或计算汇总统计的对象。看到filter详情。
Usage:
用法：
filter(flowFrame, filter)
filter(flowFrame, filter)
split Split flowFrame object according to a filter, a filterResult or a factor. For most types of filters, an optional flowSet=TRUE parameter will create a flowSet rather than a simple list. See split for details.
分裂分割flowFrame对象根据filter，filterResult或factor。对于大多数类型的过滤器，一个可选的：flowSet=TRUE参数将创建一个，而不是一个简单的列表flowSet。看到split详情。
Usage:
用法：
split(flowFrame, filter, flowSet=FALSE, ...)
split(flowFrame, filter, flowSet=FALSE, ...)
split(flowFrame, filterResult, flowSet=FALSE, ...)
split(flowFrame, filterResult, flowSet=FALSE, ...)
split(flowFrame, factor, flowSet=FALSE, ...)
split(flowFrame, factor, flowSet=FALSE, ...)
Subset Subset a flowFrame according to a filter or a logical vector. The same can be done using the standard subsetting operator with a filter, filterResult, or a logical vector as first argument.
子集的一个子集flowFramefilter或逻辑向量。同样可以使用标准的子集运算符与filter，filterResult，或作为第一个参数的逻辑向量。
Usage:
用法：
Subset(flowFrame, filter)
Subset(flowFrame, filter)
Subset(flowFrame, logical)
Subset(flowFrame, logical)
cbind2 Expand a flowFrame by the data in a numeric matrix of the same length. The matrix must have column names different from those of the flowFrame. The additional method for numerics only raises a useful error message.
cbind2展开由一个相同长度的flowFrame数据的numeric matrix。 matrix必须有flowFrame不同的列名。 numerics只提出了一个有用的错误消息的其他方法。
Usage:
用法：
cbind2(flowFrame, matrix)
cbind2(flowFrame, matrix)
cbind2(flowFrame, numeric)
cbind2(flowFrame, numeric)
compensate Apply a compensation matrix (or a compensation object) on a flowFrame object. This returns a compensated flowFrame.
补偿的补偿矩阵（或compensation对象）申请flowFrame对象。这将返回一个补偿flowFrame。
Usage:
用法：
compensate(flowFrame, matrix) compensate(flowFrame, data.frame)
compensate(flowFrame, matrix) compensate(flowFrame, data.frame)
spillover Extract spillover matrix from description slot if present.
摘录描述插槽，如果存在溢出溢出矩阵。
Usage:
用法：
spillover(flowFrame, matrix)
spillover(flowFrame, matrix)
== Test equality between two flowFrames
==测试平等之间两个flowFrames
<, >, <=, >= These operators basically treat the
<，>，<=，> =，这些运营商基本上治疗
initialize(flowFrame): Object instantiation, used
initialize(flowFrame)：对象实例，使用
作者（S）----------Author(s)----------
F. Hahne, B. Ellis, P. Haaland and N. Le Meur
参见----------See Also----------
flowSet, read.FCS
flowSet，read.FCS
举例----------Examples----------
## load example data[＃加载数据为例]
data(GvHD)
frame <- GvHD[[1]]
## subsetting[＃子集]
frame[1:4,]
frame[,3]
frame[,"FSC-H"]
frame$"SSC-H"
## accessing and replacing raw values[＃访问和替换原始值]
head(exprs(frame))
exprs(frame) <- exprs(frame)[1:3000,]
frame
exprs(frame) <- exprs(frame)[,1:6]
frame
## access FCS keywords[＃访问FCS的关键字]
head(description(frame))
keyword(frame, c("FILENAME", "$FIL"))
## parameter annotation[＃参数注释]
parameters(frame)
pData(parameters(frame))
## summarize frame data[＃总结帧数据。]
summary(frame)
## plotting[＃绘制]
plot(frame)
if(require(flowViz)){
plot(frame)
plot(frame, c("FSC-H", "SSC-H"))
plot(frame[,1])
plot(frame, c("FSC-H", "SSC-H"), smooth=FALSE)
}
## frame dimensions[＃帧尺寸]
ncol(frame)
nrow(frame)
dim(frame)
## accessing and replacing parameter names[＃访问和替换参数名称]
featureNames(frame)
all(featureNames(frame) == colnames(frame))
colnames(frame) <- make.names(colnames(frame))
colnames(frame)
parameters(frame)$name
names(frame)
## accessing a GUID[＃访问GUID]
identifier(frame)
identifier(frame) <- "test"
## dynamic range of a frame[＃一帧的动态范围]
range(frame)
range(frame, "FSC.H", "FL1.H")
range(frame)$FSC.H
## iterators[＃迭代]
head(each_row(frame, mean))
head(each_col(frame, mean))
## transformation[＃转换]
opar <- par(mfcol=c(1:2))
if(require(flowViz))
plot(frame, c("FL1.H", "FL2.H"))
frame <- transform(frame, FL1.H=log(`FL1.H`), FL2.H=log(`FL2.H`))
if(require(flowViz))
plot(frame, c("FL1.H", "FL2.H"))
par(opar)
range(frame)
## filtering of flowFrames[＃过滤的flowFrames]
rectGate <- rectangleGate(filterId="nonDebris","FSC.H"=c(200,Inf))
fres <- filter(frame, rectGate)
summary(fres)
## splitting of flowFrames[＃的flowFrames分裂]
split(frame, rectGate)
split(frame, rectGate, flowSet=TRUE)
split(frame, fres)
f <- cut(exprs(frame$FSC.H), 3)
split(frame, f)
## subsetting according to filters and filter results[＃子集过滤器和过滤结果]
Subset(frame, rectGate)
Subset(frame, fres)
Subset(frame, as.logical(exprs(frame$FSC.H) < 300))
frame[rectGate,]
frame[fres,]
## accessing the spillover matrix[＃访问外溢矩阵]
try(spillover(frame))
## check equality[＃检查平等]
frame2 <- frame
frame == frame2
exprs(frame2) <- exprs(frame)*2
frame == frame2
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 17:43:25
