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

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readMSnSet(MSnbase)
readMSnSet()所属R语言包：MSnbase

                                         Read 'MSnSet'
                                         读“MSnSet

                                         译者：生物统计家园网 机器人LoveR

描述----------Description----------

This function reads data files to generate an MSnSet instance. It is a wrapper around Biobase's readExpressionSet function with an additional  featureDataFile parameter to include feature data. See also readExpressionSet for more details.  
该函数读取数据文件的产生MSnSet实例。这是一个围绕BIOBASE的readExpressionSet函数与一个额外的featureDataFile参数包括特征数据的包装。也看到readExpressionSet更多细节。


用法----------Usage----------


readMSnSet(exprsFile,
           phenoDataFile,
           featureDataFile,
           experimentDataFile,
           notesFile,
           path, annotation,
           exprsArgs = list(sep = sep, header = header, row.names = row.names, quote = quote, ...),
           phenoDataArgs = list(sep = sep, header = header, row.names = row.names, quote = quote, stringsAsFactors = stringsAsFactors, ...),
           featureDataArgs = list(sep = sep, header = header, row.names = row.names, quote = quote, stringsAsFactors = stringsAsFactors, ...),
           experimentDataArgs = list(sep = sep, header = header, row.names = row.names, quote = quote, stringsAsFactors = stringsAsFactors, ...),
           sep = "\t",
           header = TRUE,
           quote = "",
           stringsAsFactors = FALSE,
           row.names = 1L,
           widget = getOption("BioC")$Base$use.widgets, ...)



参数----------Arguments----------

参数：exprsFile
(character) File or connection from which to read expression values. The file should contain a matrix with rows as features and columns as samples. read.table is called with this as its file argument and further arguments given by exprsArgs.   
（字符）的文件或连接，从中读取表达式的值。该文件应包含与功能的行和列作为样本矩阵。 read.table这被称为其file参数，并给予进一步的论据exprsArgs。


参数：phenoDataFile
(character) File or connection from which to read phenotypic data. read.AnnotatedDataFrame is called with this as its file argument and further arguments given by phenoDataArgs.  
（字符）的文件或从中读取的表型数据的连接。 read.AnnotatedDataFrame这被称为其file参数，并给予进一步的论据phenoDataArgs。


参数：experimentDataFile
(character) File or connection from which to read experiment data. read.MIAME is called with this as its file argument and further arguments given by experimentDataArgs.  
（字符）的文件或从中读取实验数据的连接。 read.MIAME这被称为其file参数，并给予进一步的论据experimentDataArgs。


参数：notesFile
(character) File or connection from which to read notes; readLines is used to input the file.
（字符）的文件或连接阅读笔记; readLines用来输入文件。


参数：path
(optional) directory in which to find all the above files.
（可选）在其中找到所有上述文件的目录。


参数：annotation
(character) A single character string indicating the annotation associated with this ExpressionSet.  
（字符）的单字符字符串，指示与此ExpressionSet关联的注解。


参数：exprsArgs
A list of arguments to be used with read.table when reading in the expression matrix.
read.table在表达矩阵读取时使用的参数列表。


参数：phenoDataArgs
A list of arguments to be used (with read.AnnotatedDataFrame) when reading the phenotypic data.
（read.AnnotatedDataFrame）用于读表型数据时的参数列表。


参数：experimentDataArgs
A list of arguments to be used (with read.MIAME) when reading the experiment data.
要使用（用read.MIAME）阅读实验数据时的参数列表。


参数：sep, header, quote, stringsAsFactors, row.names
arguments used by the read.table-like functions.
read.table类似的功能使用的参数。


参数：widget
A boolean value indicating whether widgets can be used. Widgets are NOT yet implemented for read.AnnotatedDataFrame.
一个布尔值指示是否可用于部件。 read.AnnotatedDataFrame部件尚未实现。


参数：...
Further arguments that can be passed on to the read.table-like functions.
read.table类似的功能，可以通过进一步的论据。


参数：featureDataFile
(character) File or connection from which to read feature data. read.AnnotatedDataFrame is called with this as its file argument and further arguments given by phenoDataArgs.  
（字符）的文件或连接，从中读取数据的功能。 read.AnnotatedDataFrame这被称为其file参数，并给予进一步的论据phenoDataArgs。


参数：featureDataArgs
A list of arguments to be used (with read.AnnotatedDataFrame) when reading the phenotypic data.   
（read.AnnotatedDataFrame）用于读表型数据时的参数列表。


值----------Value----------

An instance of the MSnSet class.
MSnSet类的一个实例。


作者（S）----------Author(s)----------



Laurent Gatto <lg390@cam.ac.uk>




举例----------Examples----------


## Not run: [＃无法运行：]
exprsFile <- "path_to_intensity_file.csv"
fdatafile <- "path_to_featuredata_file.csv"
pdatafile <- "path_to_sampledata_file.csv"
## Read ExpressionSet with appropriate parameters[＃读取相应的参数ExpressionSet]
res <- readMSnSet(exprsFile, pdataFile, fdataFile, sep = "\t", header=TRUE)


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