R语言 flowWorkspace包 GatingHierarchy-class()函数中文帮助文档(中英文对照)

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GatingHierarchy-class(flowWorkspace)
GatingHierarchy-class()所属R语言包：flowWorkspace

                                        Class "GatingHierarchy"
                                         类“GatingHierarchy”

                                         译者：生物统计家园网 机器人LoveR

描述----------Description----------

GatingHierarchy is a class for representing the gating hierarchy imported from a flowJo workspace.
GatingHierarchy是一类为代表门层次从flowJo工作区进口。


Details

详情----------Details----------

There is a one-to-one correspondence between GatingHierarchy objects and FCS files in the flowJo workspace. Each sample (FCS file) is associated with it's own GatingHierarchy. This is different from the workflow representation used in flowCore.
是GatingHierarchy对象和FCS的文件在flowJo工作区之间有一个一一对应。每个样本（FCS的文件）是与它自己的GatingHierarchy。这是不同的从在flowCore使用的工作流表示。

A GatingHierarchy can have two “states”. After a call to parseWorkspace(...,execute=FALSE), the workspace is imported but the data is not. A call to execute() is needed in order to load, transform, compensate, and gate the associated data. Alternately, one may call parseWorkspace(...,execute=TRUE). Whether or not a GatingHierarchy has been applied to data is encoded in the flag slot. Some methods will warn the user, or may not function correctly if the GatingHierarchy has not been execute()d.This mechanism is in place, largely for the purpose of memory efficiency when working with larger workspaces. It allows the use to load a workspace and subset desired samples before proceeding to load the data. If one has netCDF 4 library installed, then memory is no longer an issue.
一个GatingHierarchy可以有两个“国家”。经过调用parseWorkspace（...，执行= FALSE），工作区是进口的，但数据是没有的。呼叫执行（）是必要的，以便加载，转换，补偿，门的相关数据。另外，可致电parseWorkspace（...，执行= TRUE）。 flag插槽与否GatingHierarchy已应用于数据编码。有些方法会向用户发出警告，或可能无法正常工作如果的GatingHierarchy没有被执行（）四，本机制到位，内存效率的目的主要是与较大的工作区的工作时。它允许使用之前，加载数据加载工作区和子集所需样品。如果你有NetCDF的4库安装，那么内存不再是一个问题。

Given a GatingHierarchy, one can extract the data associated with any subpopulation, extract gates, plot gates, and extract population proportions. This facilitates the comparison of manual gating methods with automated gating algorithms.
鉴于一个GatingHierarchy，可以提取任何人群的相关数据，提取大门，小区大门，提取的人口比例。这有利于手动门自动门控算法方法的比较。

GatingHierarchy objects can be converted to workflows.
GatingHierarchy对象可以转换为工作流。


类的对象----------Objects from the Class----------

GatingHierarchy objects are elements of a GatingSet, which is returned by a call to parseWorkspace().
GatingHierarchy对象一个GatingSet的元素，这是由parseWorkspace()调用返回。


插槽----------Slots----------




tree: Object of class "graphNEL" representing the tree-structured gating hierarchy.
tree类"graphNEL"代表树结构浇注层次的对象。




nodes: Object of class "character". A vector of node names representing the populations/gates in the tree.
nodes类"character"的对象。一个向量代表的人口/盖茨在树的节点名称。




name: Object of class "character". The name of the sample. Usually the FCS filename, but it depends on how it was defined in the flowJo workspace.
name类"character"的对象。样品名称。通常情况下，FCS文件名，但是这取决于它是如何定义在flowJo工作区。




flag: Object of class "logical". A flag indicating whether the gates, transformations, and compensation matrices have been applied to data, or simply imported.
flag类"logical"的对象。一个标志，指示的大门，转换和补偿矩阵是否已应用于数据，或者干脆进口。




transformations: Object of class "list". The list of transformations applied to each dimension of the data.
transformations类"list"的对象。应用于数据的每个维度的转换列表。




compensation: Object of class "matrix". The compensation matrix applied to the data
compensation类"matrix"的对象。补偿矩阵应用于数据




dataPath: Object of class "character". A path to the fcs file associated with this GatingHierarchy
dataPath类"character"的对象。一个功能界别的文件的路径与此GatingHierarchy相关




isNcdf: Specifies if the netcdf is used to store the data for this object.
isNcdf：如果NetCDF的被指定用于存储此对象的数据。


方法----------Methods----------




[[<- signature(x = "GatingSet", i = "ANY", j = "ANY", value = "GatingHierarchy"): replacement method for GatingHierarchy objects within a GatingSet
[< - signature(x = "GatingSet", i = "ANY", j = "ANY", value = "GatingHierarchy")：内GatingSet的GatingHierarchy对象的替换方法




execute signature(hierarchy = "GatingHierarchy"): Apply the compensation, transformation, and gating of a GatingHierarchy to its associated fcs file.
执行signature(hierarchy = "GatingHierarchy")：申请赔偿，改造，一个及其相关功能界别的文件GatingHierarchy门。




flowWorkspace2flowCore signature(obj = "GatingHierarchy"): convert a GatingHierarchy to a flowCore workflow.
flowWorkspace2flowCoresignature(obj = "GatingHierarchy")：转换到flowCore工作流程GatingHierarchy的。




getBoundaries signature(obj = "GatingHierarchy", y = "character"): Get the vertices of gate y in GatingHierarchy obj.
getBoundariessignature(obj = "GatingHierarchy", y = "character")：获取在GatingHierarchy obj的门&#376;的顶点。




getChildren signature(obj = "GatingHierarchy", y = "character"): Get the child nodes of population y in obj.
的getChildrensignature(obj = "GatingHierarchy", y = "character")：人口&#376;获取obj的子节点。




getData signature(obj = "GatingHierarchy"): Return a flowFrame for population y in GatingHierarchy obj.
的getDatasignature(obj = "GatingHierarchy")：返回一个人口在GatingHierarchy OBJ&#376;flowFrame。




getDimensions signature(obj = "GatingHierarchy", y = "character"): Get the dimensions for the gate of population y
getDimensionssignature(obj = "GatingHierarchy", y = "character")：获取人口&#376;门的尺寸




getGate signature(obj = "GatingHierarchy", y = "character"): Return the gate for population y.
getGatesignature(obj = "GatingHierarchy", y = "character")：返回人口&#376;门。




getGate signature(obj = "GatingHierarchy", y = "numeric"): REturn the gate for population y, by index rather than name.
getGatesignature(obj = "GatingHierarchy", y = "numeric")：返回&#376;人口的大门，由指数，而不是名称。




getIndices signature(obj = "GatingHierarchy", y = "character"): Return the event membership indices for population y.
getIndicessignature(obj = "GatingHierarchy", y = "character")：返回事件成员的人口&#376;指数。




getKeywords signature(obj = "GatingHierarchy", y = "missing"): Return the keywords for the GatingHierarchy
getKeywordssignature(obj = "GatingHierarchy", y = "missing")：返回关键字的GatingHierarchy




getNodes signature(x = "GatingHierarchy"): Return the node list for the gating hierarchy.
getNodessignature(x = "GatingHierarchy")：返回浇注层次的节点列表。




getParent signature(obj = "GatingHierarchy", y = "character"): Get the parent node of a population.
的getParentsignature(obj = "GatingHierarchy", y = "character")：人口的父节点。




getParent signature(obj = "GatingHierarchy", y = "numeric"):  Get the parent node of a population, by index.
的getParentsignature(obj = "GatingHierarchy", y = "numeric")：指数由人口的父节点。




getPopStats signature(x = "GatingHierarchy"): Return a table of population statistics (proportions and counts) for a gating hierarchy
getPopStatssignature(x = "GatingHierarchy")：返回一个门层次的人口统计数字表（比例和数量）




getProp signature(x = "GatingHierarchy", y = "character"): return the population proportion for population y.
getPropsignature(x = "GatingHierarchy", y = "character")：返回&#376;人口的人口比例。




getSample signature(x = "GatingHierarchy"): Return the sample name of the gating hierarchy
getSamplesignature(x = "GatingHierarchy")：返回浇注层次的样品名称




getTotal signature(x = "GatingHierarchy", y = "character"): get the total number of events in population y
的getTotalsignature(x = "GatingHierarchy", y = "character")：&#376;事件在人口总数




keyword signature(object = "GatingHierarchy", keyword = "character"): get a specific keyword from the gating hierarchy
关键字signature(object = "GatingHierarchy", keyword = "character")：从浇注层次的特定关键字




plot signature(x = "GatingHierarchy", y = "missing"): plot a gating hierarchy graph
图signature(x = "GatingHierarchy", y = "missing")：绘制门的层次结构图




plotGate signature(x = "GatingHierarchy", y = "character"): plot a manual gate for the population over the parent data.
plotGatesignature(x = "GatingHierarchy", y = "character")：图一个人口超过父数据的手动门。




plotGate signature(x = "GatingHierarchy", y = "numeric"): plot a manual gate for a population referenced by index, over the parent data
plotGatesignature(x = "GatingHierarchy", y = "numeric")：通过索引引用的人口为手动门小区，在父数据




plotPopCV signature(x = "GatingHierarchy"): plot the coefficient of variation for all populations, between flowCore and flowJo counts.
plotPopCVsignature(x = "GatingHierarchy")：图的所有人群之间的变异系数flowCore和flowJo计数。




show signature(object = "GatingHierarchy"):  Summarize a Gating Hierarchy
显示signature(object = "GatingHierarchy")：总结了浇注层次


作者（S）----------Author(s)----------



Greg Finak &lt;gfinak@fhcrc.org&gt;




参考文献----------References----------



参见----------See Also----------

parseWorkspace GatingSet
parseWorkspaceGatingSet


举例----------Examples----------


        require(flowWorkspaceData)
        d<-system.file("extdata",package="flowWorkspaceData")
        wsfile<-list.files(d,pattern="A2004Analysis.xml",full=TRUE)
        ws <- openWorkspace(wsfile);
        G<-try(parseWorkspace(ws,execute=TRUE,path=d,name=1));
        getPopStats(G[[1]]);
        plotPopCV(G[[1]])
        plotGate(G[[1]],getNodes(G[[1]])[4]);
        getGate(G[[1]],getNodes(G[[1]])[4]);
        getBoundaries(G[[1]],getNodes(G[[1]])[4])
        getData(G[[1]],getNodes(G[[1]])[4])

转载请注明:出自 生物统计家园网(http://www.biostatistic.net)。


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