read.FCS(flowCore)
read.FCS()所属R语言包：flowCore
Read an FCS file
读取FCS文件
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Check validity and Read Data File Standard for Flow Cytometry
检查的有效性和流式单元仪读取数据文件的标准
用法----------Usage----------
isFCSfile(files)
read.FCS(filename, transformation="linearize", which.lines=NULL,
alter.names=FALSE, column.pattern=NULL,
decades=0, ncdf = FALSE, min.limit=NULL, dataset=NULL)
cleanup()
参数----------Arguments----------
参数：files
A vector of filenames
一个文件名的向量
参数：filename
Character of length 1: filename
字符长度为1：文件名
参数：transformation
An character string that defines the type of transformation. Valid values are linearize (default) or scale.The linearize transformation applies the appropriate power transform to the data while the scale transformation scales all columns to $[0,10^decades]$. defaulting to decades=0 as in the FCS4 specification. A logical can also be used: TRUE is equal to linearize and FALSE corresponds to no transformation.
定义一个字符串类型的转换。有效的值是linearize（默认）或scalelinearize改造，运用适当的电源转换数据，而所有的scale改造规模列[0,10美元^十年]。默认为十年= 0在FCS4规范。也可以被用来逻辑：TRUE等于linearize和FALSE相当于没有改造。
参数：which.lines
Numeric vector to specify the indices of the lines to be read. If NULL all the records are read, if of length 1, a random sample of the size indicated by which.lines is read in.
要读取的数字向量，以指定行的指数。如果为NULL读取所有的记录，表示如果which.lines读入的长度为1，随机抽样的大小
参数：alter.names
boolean indicating whether or not we should rename the columns to valid R names using make.names. The default is FALSE.
布尔值，指示，我们是否应该重新命名的列有效的的ř名称，使用make.names。默认值为FALSE。
参数：column.pattern
An optional regular expression defining parameters we should keep when loading the file. The default is NULL.
一个可选的正则表达式定义的参数，我们应该保持加载文件时。默认值为NULL。
参数：decades
When scaling is activated, the number of decades to use for the output.
缩放时被激活，数十年来使用的输出。
参数：ncdf
Instead of reading all data into memory, this switches to file-based data storage. A netCDF file is creates for each flowFrame in the .flowCoreNcdf subdirectory. For large data sets this significantly reduces the memory profile of the R session, to the cost of speed and disk space. The exprs and exprs<- methods make sure that the user always gets a matrix of data values. Please note that currently all operations that call exprs<-, either explicitly or implicitely, will result in the creation of a new netCDF file. This behaviour may change in the future. Currently the software does not remove any of the netCDF files and it is up to the user to do clean up. The easiest way to do that is to delete the whole netCDF directory. To this end, one can invoke the cleanup function.
而不是所有的数据读入内存，切换到基于文件的数据存储。一个netCDF文件创建的每个flowFrame.flowCoreNcdf子目录。对于大型数据集，这大大降低了R会话的内存配置文件，速度和磁盘空间的成本。 exprs和exprs<-方法确保用户总是得到一个数据值的矩阵。请注意，目前所有的操作调用exprs<-，明示或implicitely，将导致创建一个新的netCDF文件中。这种行为可能会在未来改变。目前该软件不删除任何netCDF文件，它是由用户做清理。做到这一点的最简单的方法是删除整个netCDF目录。为此，我们可以调用cleanup功能。
参数：min.limit
The minimum value in the data range that is allowed. Some instruments produce extreme artifactual values. The positive data range for each parameter is completely defined by the measurement range of the instrument and all larger values are set to this threshold. The lower data boundary is not that well defined, since compensation might shift some values below the original measurement range of the instrument. The default value of -111 copies the behavior of flowJo. It can be set to an arbitrary number or to NULL, in which case the original values are kept.
在数据范围允许的最低值。一些仪器的值产生极端artifactual的。积极为每个参数的数据范围完全由仪器的测量范围和定义，所有较大的值设置为这个阈值。较低的数据边界没有明确界定，因为补偿可能会转移一些值低于原仪器测量范围。默认值-111复制行为flowJo，。它可以设置任意数量或NULL，在这种情况下，保持原来的值。
参数：dataset
The FCS file specification allows for multiple data segments in a single file. Since the output of read.FCS is a single flowFrame we can't automatically read in all available sets. This parameter allows to chose one of the subsets for import. Its value is supposed to be an integer in the range of available data sets. This argument is ignored if there is only a single data segment in the FCS file.
FCS文件规范允许在一个文件中的多个数据段。由于的read.FCS输出是一个单一的flowFrame我们不能自动读取所有可用的集。此参数允许选择进口的亚群之一。它的价值应该是在现有数据集范围内的整数。此参数将被忽略，如果只有一个单一的数据段在FCS文件。
Details
详情----------Details----------
The function isFCSfile determines whether its arguments are valid FCS files.
功能isFCSfile确定其参数是否有效FCS文件。
The function read.FCS works with the output of the FACS machine software from a number of vendors (FCS 2.0, FCS 3.0 and List Mode Data LMD). However, the FCS 3.0 standard includes some options that are not yet implemented in this function. If you need extensions, please let me know. The output of the function is an object of class flowFrame.
与流式单元仪机软件供应商的数量（FCS的FCS的2.0，3.0和列表模式数据LMD的）从输出的功能read.FCS。然而，FCS 3.0标准包括一些尚未实现此功能的选项。如果您需要扩展，请让我知道。该函数的输出是一个类flowFrame的对象。
For specifications of FCS 3.0 see http://www.isac-net.org and the file ../doc/fcs3.html in the doc directory of the package.
FCS的3.0规格，http://www.isac-net.org和doc包目录中的文件.. / doc/fcs3.html的。
The nlines and sampling arguments allow you to read a subset of the record as you might not want to read the thousands of events recorded in the FCS file.
nlines和sampling参数允许你读取记录的一个子集，你可能不想读成千上万FCS的文件中记录的事件。
The which.lines argument allows you to read a specific number of records.
which.lines参数，使您可以读取的记录的具体数量。
值----------Value----------
isFCSfile returns a logical vector.
isFCSfile返回一个逻辑的向量。
read.FCS returns an object of class flowFrame that contains the data in the exprs slot, the parameters monitored in the parameters slot and the keywords and value saved in the header of the FCS file.
read.FCS返回一个类的对象flowFrame包含在exprs插槽的数据，监测参数parameters插槽和关键字和值保存在头FCS的文件。
作者（S）----------Author(s)----------
F. Hahne, N.Le Meur
参见----------See Also----------
read.flowSet
read.flowSet
举例----------Examples----------
## a sample file[＃示例文件]
fcsFile <- system.file("extdata", "0877408774.B08", package="flowCore")
## read file and linearize values[＃读取文件和线性值]
samp <- read.FCS(fcsFile, transformation="linearize")
exprs(samp[1:3,])
description(samp)[3:6]
class(samp)
## Only read in lines 2 to 5[＃只读取行中2至5]
subset <- read.FCS(fcsFile, which.lines=2:5, transformation="linearize")
exprs(subset)
## Read in a random sample of 100 lines[在随机抽样的100线＃读取]
subset <- read.FCS(fcsFile, which.lines=100, transformation="linearize")
nrow(subset)
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。
|
发表于 2012-2-25 17:47:22
