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

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parseWorkspace(flowWorkspace)
parseWorkspace()所属R语言包：flowWorkspace

                                         Parse a flowJo Workspace
                                         解析flowJo工作区

                                         译者：生物统计家园网 机器人LoveR

描述----------Description----------

Function to parse a flowJo Workspace, generate a GatingHierarchy or GatingSet object, and associated flowCore gates. The data are not loaded or acted upon until an explicit call to execute() is made on the GatingHierarchy objects in the GatingSet.
解析flowJo工作区的功能，生成一个GatingHierarchy或GatingSet对象，以及相关的flowCore门。数据不会被加载，或后execute()的GatingHierarchyGatingSet对象，直到显式调用行事。


用法----------Usage----------


## S4 method for signature 'flowJoWorkspace'
parseWorkspace(obj,name=NULL,execute=FALSE,isNcdf=FALSE,subset=NULL,nslaves=4,...)



参数----------Arguments----------

参数：obj
A flowJoWorkspace to be parsed.  
一个flowJoWorkspace被解析。


参数：name
numeric or character. The name or index of the group of samples to be imported. If NULL, the groups are printed to the screen and one can be selected interactively. Usually, multiple groups are defined in the flowJo workspace file.  
numeric或character。进口组样品的名称或指数。如果NULL，组打印到屏幕上，并可以选择交互。通常情况下，多个团体在flowJo工作区文件定义。


参数：execute
TRUE|FALSE a logical specifying if the gates, transformations, and compensation should be immediately calculated after the flowJo workspace have been imported. You should probably set this to TRUE.  
TRUE|FALSE逻辑指定已进口的大门，转换和补偿，应立即计算后flowJo工作区。你应该设置为TRUE。


参数：isNcdf
TRUE|FALSE logical specifying if you would like to use netcdf to store the data, or if you would like to keep all the flowFrames in memory. For a small data set, you can safely set this to FALSE, but for larger data, we suggest using netcdf. You will need the netcdf C library installed.  
TRUE|FALSE指定的逻辑，如果你想使用NetCDF的存储数据，或者如果您想保存在内存中的所有flowFrames。对于一个小的数据集，你可以安全地设置为FALSE，但对于更大的数据，我们建议使用NetCDF的。您将需要安装NetCDF的C库。


参数：subset
numeric vector specifying the subset of samples in a group to import.  
numeric向量组导入指定的样本子集。


参数：nslaves
numeric number of slave processes for executing the gating under Rmpi  
numeric从进程下Rmpi执行浇注


参数：...
Additional arguments. path="character" The path to the fcs files that are to be imported. The code will search recursively, so you can point it to a location above the files. This argument is mandatory.   
额外的参数。 path="character"功能界别是要导入的文件的路径。代码将递归搜索，让你可以指出上述文件的位置。这种说法是强制性的。


Details

详情----------Details----------

A flowJoWorkspace is generated with a call to openWorkspace(), passing the name of the xml workspace file. This returns a flowJoWorkspace, which can be parsed using the parseWorkspace() method. The function can be called non-interactively by passing the index or name of the group of samples to be imported via parseWorkspace(obj,name=x), where x is either the numeric index, or the name.
一个flowJoWorkspace调用openWorkspace()与产生，传递的XML workspace文件的名称。这将返回一个flowJoWorkspace使用parseWorkspace()方法，它可以被解析。功能可以通过索引或组样品的名称，可以通过parseWorkspace(obj,name=x)进口被称为非交互方式，其中x要么是数字索引，或者名称。


值----------Value----------

Returns a GatingSet, which is a wrapper around a list of GatingHierarchy objects, each representing a single sample in the workspace. The GatingHierarchy objects contain graphNEL trees that  represent the gating hierarchy of each sample. Each node in the GatingHierarchy has associated data, including the population counts from flowJo, the parent population counts, the flowCore gates generated from the flowJo workspace gate definitions. Data are not yet loaded or acted upon at this stage. To execute the gating of each data file, a call to execute() must be made on each GatingHierarchy object in the GatingSet. These can be iterated over using lapply(). Options to execute() allow the user to specify whether compensated and transformed data should be kept in memory for each sample, whether indices specifying the population membership of each event at each node in the GatingHierarchy should be kept in memory, or whether these should be deleted after each node is processed and only summary statistics kept associated with each population. The latter option forgoes the ability to plot the data, and is more useful in a high–throughput, large scale setting where keeping the data around in memory can be inefficient.
返回GatingSet，这是周围GatingHierarchy对象，每个代表在工作区中的一个样本名单的包装。 GatingHierarchy对象包含的graphNEL树表示每个样品门层次。每个在GatingHierarchy节点有关联的数据，包括从flowJo工作区大门定义flowCore盖茨flowJo，家长的人口数，人口产生计数。数据尚未加载，在这个阶段后，或担任。执行每个数据文件的门，execute()呼叫必须在GatingHierarchy每GatingSet对象。这些都可以使用lapply()遍历。选项execute()允许用户指定是否补偿和转换后的数据应保持在每个样品的内存，指数在每个GatingHierarchy节点指定每个事件的人口成员是否应保存在内存中或是否应该被删除每个节点处理后，只有汇总统计每个人口保持。选择后者放弃绘制数据的能力，是一种高通量，大规模的设置保持在内存中的数据可以是低效更为有用。


作者（S）----------Author(s)----------



Greg Finak <a href="mailto:gfinak@fhcrc.org">gfinak@fhcrc.org</a>




参考文献----------References----------



参见----------See Also----------

getSampleGroups
getSampleGroups


举例----------Examples----------


## Not run: [＃无法运行：]
        #f is a xml file name of a flowJo workspace[f是一个XML文件的名称一个flowJo工作区]
        ws<-openWorkspace(f)
        G&lt;-parseWorkspace(ws,execute=TRUE,isNcdf=FALSE,path="."); #assume that the fcs files are below the current directory.[假设，FCS文件是当前目录下。]
        #G is a GatingSet.[G是GatingSet。]


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


注：
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