flowSet-class(flowCore)
flowSet-class()所属R语言包：flowCore
'flowSet': a class for storing flow cytometry raw data from
“flowSet”：一类储存流式单元仪从原始数据
译者：生物统计家园网 机器人LoveR
描述----------Description----------
This class is a container for a set of
这个类是一组的容器
创建对象----------Creating Objects----------
Objects can be created using<br> new('flowSet',<br> frames = ...., # environment with flowFrames<br> phenoData = .... # object of class AnnotatedDataFrame<br> colnames = .... # object of class character<br> )<br>
可以创建对象使用参考 new('flowSet',参考 frames = ...., # environment with flowFrames参考 phenoData = .... # object of class AnnotatedDataFrame参考 colnames = .... # object of class character参考 )参考
or via the constructor flowSet, which takes arbitrary numbers of flowFrames, either as a list or directly as arguments, along with an optional AnnotatedDataFrame for the phenoData slot and a character scalar for the name by which the object can be referenced.
或通过构造flowSet，这需要任意数量flowFrames的，无论是作为一个列表，或直接作为参数，随着一个可选的AnnotatedDataFramephenoData插槽和一个character的标为name可以参考的对象。
flowSet(..., phenoData)
flowSet(..., phenoData)
Alternatively, flowSets can be coerced from list and environment objects.
另外，flowSets可以强制list和environment对象。
as(list("A"=frameA,"B"=frameB),"flowSet")
as(list("A"=frameA,"B"=frameB),"flowSet")
The safest and easiest way to create flowSets directly from <acronym>FCS</acronym> files is via the read.flowSet function, and there are alternative ways to specify the files to read. See the separate documentation for details.
flowSet</>的缩写文件FCS的直接从<acronym>创建最安全和最简单的方法是通过read.flowSet功能，并有替代方式，到指定的文件读取。有关详细信息，请参阅单独的文档。
插槽----------Slots----------
frames: An environment
frames：environment
phenoData: A AnnotatedDataFrame containing the phenotyoic data for the whole data set. Each row corresponds to one of the flowFrames in the frames slot. The sampleNames of phenoData (see below) must match the names of the flowFrame in the frames environment.
phenoData：AnnotatedDataFrame包含整个数据集phenotyoic数据。每一行对应到flowFrame插槽frames的一个。 sampleNamesphenoData（见下文）必须符合中flowFrame环境frames的名字。
colnames: A character object with the (common) column names of all the data matrices in the
colnames：character对象（普通）中的所有数据矩阵的列名
方法----------Methods----------
[, [[ Subsetting. x[i] where i is a scalar, returns a flowSet object, and x[[i]] a flowFrame object. In this respect the semantics are similar to the behavior of the subsetting operators for lists. x[i, j] returns a flowSet for which the parameters of each flowFrame have been subset according to j, x[[i,j]] returns the subset of a single flowFrame for all parameters in j. Similar to data frames, valid values for i and j are logicals, integers and characters.
[[子集。 x[i]i是一个标量，返回一个flowSet对象，x[[i]]flowFrame对象。在这方面的语义是类似列表的子集经营者的行为。 x[i, j]返回一个flowSet每个flowFrame已经子集j，x[[i,j]]返回一个单一的flowFrame子集的参数在j所有参数。类似的数据框，i和j是逻辑值，整数和字符的有效值。
Usage:
用法：
flowSet[i]
flowSet[i]
flowSet[i,j]
flowSet[i,j]
flowSet[[i]]
flowSet[[i]]
\$ Subsetting by frame name. This will return a single flowFrame object. Note that names may have to be quoted if they are no valid R symbols
\ $子集框架的名称。这将返回一个单一的flowFrame对象。请注意，名称可能被引用，如果他们是没有有效ŕ符号
colnames, colnames<- Extract or replace the colnames slot.
colnames，colnames < - 提取或替换colnames插槽。
Usage:
用法：
colnames(flowSet)
colnames(flowSet)
colnames(flowSet) <- value
colnames(flowSet) <- value
identifier, identifier<- Extract or replace the name item from the environment.
标识符，标识符< - 提取或更换环境name项目。
Usage:
用法：
identifier(flowSet)
identifier(flowSet)
identifier(flowSet) <- value
identifier(flowSet) <- value
phenoData, phenoData<- Extract or replace the AnnotatedDataFrame from the phenoData slot.
phenoData，phenoData < - AnnotatedDataFrame插槽phenoData从提取或更换。
Usage:
用法：
phenoData(flowSet)
phenoData(flowSet)
phenoData(flowSet) <- value
phenoData(flowSet) <- value
pData, pData<- Extract or replace the data frame (or columns thereof) containing actual phenotypic information from the phenoData slot.
PDATA，PDATA < - 提取或替换的数据框（或列）phenoData插槽包含实际的表型信息。
Usage:
用法：
pData(flowSet)
pData(flowSet)
pData(flowSet)$someColumn <- value
pData(flowSet)$someColumn <- value
varLabels, varLabels<- Extract and set varLabels in the AnnotatedDataFrame of the phenoData slot.
varLabels，varLabels < - 提取和设置在的AnnotatedDataFrame插槽phenoData varLabels。
Usage:
用法：
varLabels(flowSet)
varLabels(flowSet)
varLabels(flowSet) <- value
varLabels(flowSet) <- value
sampleNames Extract and replace sample names from the phenoData object. Sample names correspond to frame identifiers, and replacing them will also replace the GUID slot for each frame. Note that sampleName need to be unique.
sampleNames提取和替换从phenoData对象样本名。样品名称对应帧标识符，并取代他们也将更换为每个帧GUID插槽。注意sampleName必须是唯一的。
Usage:
用法：
sampleNames(flowSet)
sampleNames(flowSet)
sampleNames(flowSet) <- value
sampleNames(flowSet) <- value
keyword Extract or replace keywords specified in a character vector or a list from the description slot of each frame. See keyword for details.
关键字提取或替换字符向量或description每一帧的时隙列表中指定的关键字。看到keyword详情。
Usage:
用法：
keyword(flowSet, list(keywords))
keyword(flowSet, list(keywords))
keyword(flowSet, keywords)
keyword(flowSet, keywords)
keyword(flowSet) <- list(foo="bar")
keyword(flowSet) <- list(foo="bar")
length number of flowFrame objects in the set.
长度数flowFrame集合中的对象。
Usage:
用法：
length(flowSet)
length(flowSet)
show display object summary.
显示对象总结。
summary Return descriptive statistical summary (min, max, mean and quantile) for each channel of each flowFrame
总结每个通道每个flowFrame返回的描述性统计摘要（最小值，最大值，平均值和位数）
Usage:
用法：
summary(flowSet)
summary(flowSet)
fsApply Apply a function on all frames in a flowSet object. Similar to sapply, but with additional parameters. See separate documentation for details.
fsApply应用flowSet对象上所有的帧的功能。 sapply类似，但与其他参数。有关详情，请参阅单独的文档。
Usage:
用法：
fsApply(flowSet, function, ...)
fsApply(flowSet, function, ...)
fsApply(flowSet, function, use.exprs=TRUE, ...)
fsApply(flowSet, function, use.exprs=TRUE, ...)
compensate Apply a compensation matrix on all frames in a flowSet object. See separate documentation for details.
补偿申请在flowSet对象的上所有帧的补偿矩阵。有关详情，请参阅单独的文档。
Usage:
用法：
compensate(flowSet, matrix)
compensate(flowSet, matrix)
transform Apply a transformation function on all frames of a flowSet object. See separate documentation for details.
变换应用对flowSet对象的所有帧转换功能。有关详情，请参阅单独的文档。
Usage:
用法：
transform(flowSet, ...)
transform(flowSet, ...)
filter Apply a filter object on a flowSet object. There are methods for filters, filterSets and lists of filters. The latter has to be a named list, where names of the list items are matching sampleNames of the flowSet. See filter for details.
过滤应用flowSet对象的滤镜对象。有filter，filterSet的方法和过滤器的名单。后者是一个命名的列表，列表项的名称匹配的flowSetsampleNames。看到filter详情。
Usage:
用法：
filter(flowSet, filter)
filter(flowSet, filter)
filter(flowSet, list(filters))
filter(flowSet, list(filters))
split Split all flowSet objects according to a filter, filterResult or a list of such objects, where the length of the list has to be the same as the length of the flowSet. This returns a list of flowFrames or an object of class flowSet if the flowSet argument is set to TRUE. Alternatively, a flowSet can be split into separate subsets according to a factor (or any vector that can be coerced into factors), similar to the behaviour of split for lists. This will return a list of flowSets. See split for details.
flowSet分裂分割所有filter对象，filterResult或这些对象的列表，列表的长度是作为flowSet长度相同。这将返回一个flowFrame的列表或一个类的对象flowSet如果flowSet参数设置为TRUE。另外，flowSet可以分割成单独的子集的一个因素（或任何因素，可分为强制向量），split列表的行为类似。这将返回一个flowSet的名单。看到split详情。
Usage:
用法：
split(flowSet, filter)
split(flowSet, filter)
split(flowSet, filterResult)
split(flowSet, filterResult)
split(flowSet, list(filters))
split(flowSet, list(filters))
split(flowSet, factor)
split(flowSet, factor)
Subset Returns a flowSet of flowFrames that have been subset according to a filter or filterResult, or according to a list of such items of equal length as the flowSet.
子集返回了flowSetSflowFrame已子集根据1filter或filterResult，或根据长度相等<X等物品列表>
Usage:
用法：
Subset(flowSet, filter)
Subset(flowSet, filter)
Subset(flowSet, filterResult)
Subset(flowSet, filterResult)
Subset(flowSet, list(filters))
Subset(flowSet, list(filters))
rbind2 Combine two flowSet objects, or one flowSet and one flowFrame object.
rbind2结合两个flowSet对象，或一个flowSet和一个flowFrame对象。
Usage:
用法：
rbind2(flowSet, flowSet)
rbind2(flowSet, flowSet)
rbind2(flowSet, flowFrame)
rbind2(flowSet, flowFrame)
spillover Compute spillover matrix from a compensation set. See separate documentation for details.
外溢计算从外溢的补偿组的矩阵。有关详情，请参阅单独的文档。
存储和性能上的重要注意事项----------Important note on storage and performance----------
The bulk of the data in a flowSet object is stored in an environment, and is therefore not automatically copied when the flowSet object is copied. If x is an object of class flowSet, then the code
大部分的在flowSet对象的数据存储在environment，因此flowSet对象被复制时不会自动复制。如果x类flowSet，那么代码的对象
作者（S）----------Author(s)----------
F. Hahne, B. Ellis, P. Haaland and N. Le Meur
参见----------See Also----------
flowFrame, read.flowSet
flowFrame，read.flowSet
举例----------Examples----------
## load example data and object creation[＃加载示例数据和对象的创建]
data(GvHD)
## subsetting to flowSet[＃子集到flowSet]
set <- GvHD[1:4]
GvHD[1:4,1:2]
sel <- sampleNames(GvHD)[1:2]
GvHD[sel, "FSC-H"]
GvHD[sampleNames(GvHD) == sel[1], colnames(GvHD[1]) == "SSC-H"]
## subsetting to flowFrame[＃子集到flowFrame]
GvHD[[1]]
GvHD[[1, 1:3]]
GvHD[[1, "FSC-H"]]
GvHD[[1, colnames(GvHD[1]) == "SSC-H"]]
GvHD$s5a02
## constructor[＃构造]
flowSet(GvHD[[1]], GvHD[[2]])
pd <- phenoData(GvHD)[1:2,]
flowSet(s5a01=GvHD[[1]], s5a02=GvHD[[2]],phenoData=pd)
## colnames[＃colnames]
colnames(set)
colnames(set) <- make.names(colnames(set))
## object name[＃对象名称]
identifier(set)
identifier(set) <- "test"
## phenoData[＃phenoData]
pd <- phenoData(set)
pd
pd$test <- "test"
phenoData(set) <- pd
pData(set)
varLabels(set)
varLabels(set)[6] <- "Foo"
varLabels(set)
## sampleNames[＃sampleNames]
sampleNames(set)
sampleNames(set) <- LETTERS[1:length(set)]
sampleNames(set)
## keywords[＃关键字]
keyword(set, list("transformation"))
## length[＃长度]
length(set)
## compensation[＃补偿]
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
summary(samp[[1]])
samp <- compensate(samp, as.matrix(comp.mat))
summary(samp[[1]])
## transformation[＃转换]
opar <- par(mfcol=c(1:2))
plot(set[[1]], c("FL1.H", "FL2.H"))
set <- transform(set, FL1.H=log(FL1.H), FL2.H=log(FL2.H))
plot(set[[1]], c("FL1.H", "FL2.H"))
par(opar)
## filtering of flowSets[＃过滤的flowSets]
rectGate <- rectangleGate(filterId="nonDebris", FSC.H=c(200,Inf))
fres <- filter(set, rectGate)
class(fres)
summary(fres[[1]])
rectGate2 <- rectangleGate(filterId="nonDebris2", SSC.H=c(300,Inf))
fres2 <- filter(set, list(A=rectGate, B=rectGate2, C=rectGate, D=rectGate2))
## Splitting frames of a flowSet[＃分割帧的flowSet]
split(set, rectGate)
split(set[1:2], rectGate, populatiuon="nonDebris2+")
split(set, c(1,1,2,2))
## subsetting according to filters and filter results[＃子集过滤器和过滤结果]
Subset(set, rectGate)
Subset(set, filter(set, rectGate))
Subset(set, list(A=rectGate, B=rectGate2, C=rectGate, D=rectGate2))
## combining flowSets[＃结合flowSets]
rbind2(set[1:2], set[3:4])
rbind2(set[1:3], set[[4]])
rbind2(set[[4]], set[1:2])
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 17:43:33
