SummarizedExperiment-class(GenomicRanges)
SummarizedExperiment-class()所属R语言包：GenomicRanges
SummarizedExperiment instances
SummarizedExperiment实例
译者：生物统计家园网 机器人LoveR
描述----------Description----------
The SummarizedExperiment class is an eSet-like container where rows represent ranges of interest (as a GRanges-class) and columns represent samples (with sample data summarized as a DataFrame-class). A SummarizedExperiment contains one or more assays, each represented by a matrix of numeric or other mode.
的SummarizedExperiment类是ESET样的容器，其中行代表的利益范围（如GRanges-class）和列代表样本（样本数据总结DataFrame-class）。一个SummarizedExperiment包含一个或多个检测，每个数字或其他方式的矩阵表示。
用法----------Usage----------
## Constructors
SummarizedExperiment(assays, ...)
## S4 method for signature 'SimpleList'
SummarizedExperiment(assays, rowData = GRanges(),
colData = DataFrame(), exptData = SimpleList(), ...,
verbose = FALSE)
## S4 method for signature 'missing'
SummarizedExperiment(assays, ...)
## S4 method for signature 'list'
SummarizedExperiment(assays, ...)
## S4 method for signature 'matrix'
SummarizedExperiment(assays, ...)
## Accessors
assays(x, ..., withDimnames=TRUE)
assays(x, ...) <- value
assay(x, i, ...)
assay(x, i, ...) <- value
rowData(x, ...)
rowData(x, ...) <- value
colData(x, ...)
colData(x, ...) <- value
exptData(x, ...)
exptData(x, ...) <- value
## S4 method for signature 'SummarizedExperiment'
dim(x)
## S4 method for signature 'SummarizedExperiment'
dimnames(x)
## S4 replacement method for signature 'SummarizedExperiment,NULL'
dimnames(x) <- value
## S4 replacement method for signature 'SummarizedExperiment,list'
dimnames(x) <- value
## Subsetting
## S4 method for signature 'SummarizedExperiment'
x[i, j, ..., drop=TRUE]
## S4 replacement method for signature 'SummarizedExperiment,ANY,ANY,SummarizedExperiment'
x[i, j] <- value
参数----------Arguments----------
参数：assays
A list or SimpleList of matrix elements, or a matrix. Each element of the list must have the same dimensions, and dimension names (if present) must be consistent across elements and with the row names of rowData, colData.
一个list或SimpleList矩阵元素，或matrix。列表中的每个元素必须具有相同的尺寸和尺寸的名称（如果存在）必须是跨元素和rowData，colData行名称相一致。
参数：rowData
A GRanges or GRangesList instance describing the ranges of interest. Row names, if present, become the row names of the SummarizedExperiment. The length of the GRanges or the GRangesList must equal the number of rows of the matrices in assays.
一个GRanges或GRangesList实例，说明利益的范围。行名，如果存在，成为SummarizedExperiment行名称。长度GRanges或GRangesList必须assays矩阵的行数相等。
参数：colData
An optional DataFrame describing the samples. Row names, if present, become the column names of the SummarizedExperiment.
一个可选的DataFrame描述的样本。行名，如果存在，成为SummarizedExperiment的列名。
参数：exptData
An optional SimpleList of arbitrary content describing the overall experiment.
一个可选的SimpleList描述的整体实验中的任意内容。
参数：...
For SummarizedExperiment, S4 methods list and matrix, arguments identical to those of the SimpleList method. For assay, ... may contain withNames, which is forwarded to assays. For other accessors, ignored.
SummarizedExperiment，S4方法list和matrix，参数相同的SimpleList方法。 assay，...可能包含withNames，转发assays的。对于其他存取，忽略。
参数：verbose
A logical(1) indicating whether messages about data coercion during construction should be printed.
一个logical(1)施工期间的有关数据胁迫的消息是否应印。
参数：x
An instance of SummarizedExperiment-class.
SummarizedExperiment类的实例。
参数：i, j
For assay, assay<-, i is a integer or numeric scalar; see "Details" for additional constraints. For SummarizedExperiment, SummarizedExperiment<-, i, j are instances that can act to subset the underlying rowData, colData, and matrix elements of assays.
assay，assay<-，i是一个整数或数字标;看到“详细资料”额外的限制。 SummarizedExperiment，SummarizedExperiment<-，i，j的情况，可以采取行动的一个子集底层rowData，colData，matrix assays元素。
参数：withDimnames
A logical(1), indicating whether dimnames should be applied to extracted assay elements.
一个logical(1)，说明是否的dimnames应适用于提取法元素。
参数：drop
A logical(1), ignored by these methods.
一个logical(1)，这些方法所忽略。
参数：value
An instance of a class specified in the S4 method signature or as outlined in "Details".
在S4的方法签名，或在“详细资料”所述指定类的一个实例。
Details
详情----------Details----------
The SummarizedExperiment class is meant for numeric and other data types derived from a sequencing experiment. The structure is rectangular, like an eSet in Biobase.
SummarizedExperiment类是从测序实验所得的数据，数字和其他类型。结构是长方形的，像eSetBiobase。
The rows of a SummarizedExperiment instance represent ranges (in genomic coordinates) of interest. The ranges of interest are described by a GRanges-class or a GRangesList-class instance, accessible using the rowData function, described below. The GRanges and GRangesList classes contains sequence (e.g., chromosome) name, genomic coordinates, and strand information. Each range can be annotated with additional data; this data might be used to describe the range (analogous to annotations associated with genes in a eSet) or to summarize results (e.g., statistics of differential abundance) relevant to the range. Rows may or may not have row names; they often will not.
SummarizedExperiment实例行代表的利益范围（在基因组坐标）。感兴趣的范围，描述了一个GRanges-class或GRangesList-class实例，可使用rowData功能，如下所述。 GRanges和GRangesList类包含序列（例如，染色体）的名称，基因组的坐标，和钢绞线信息。每个范围可以注明额外的数据，这些数据可能被用来描述的范围（类似与基因相关的注释eSet）或总结的结果（例如，丰度差统计）有关范围。行可能会或可能不会有行名，他们往往不会。
Each column of a SummarizedExperiment instance represents a sample. Information about the samples are stored in a DataFrame-class, accessible using the function colData, described below. The DataFrame must have as many rows as there are columns in the SummarizedExperiment, with each row of the DataFrame providing information on the sample in the corresponding column of the SummarizedExperiment. Columns of the DataFrame represent different sample attributes, e.g., tissue of origin, etc. Columns of the DataFrame can themselves be annotated (via the values function) in a fashion similar to the varMetadata facilities of the eSet class. Column names typically provide a short identifier unique to each sample.
SummarizedExperiment实例的每一列代表一个样本。有关样品的信息存储在一个DataFrame-class，可使用的功能colData，如下所述。 DataFrame必须有许多行有SummarizedExperiment，用每个DataFrame样品提供信息，在相应列SummarizedExperiment行列。 DataFrame列代表不同样本的属性，例如，组织起源，类似的DataFrame可以自己注明（通过values函数）等列在一个时尚varMetadataeSet类的设施。列名通常提供一个简短的唯一标识符每个样品。
A SummarizedExperiment can also contain information about the overall experiment, for instance the lab in which it was conducted, the publications with which it is associated, etc. This information is stored as a SimpleList-class, accessible using the exptData function. The form of the data associated with the experiment is left to the discretion of the user.
一个SummarizedExperiment还可以包含关于整体实验的信息，例如在其中进行的实验室，与它相关的出版物等信息存储SimpleList-class，使用访问exptData功能。与实验相关的数据的形式留给用户自行决定。
The SummarizedExperiment is appropriate for matrix-like data. The data are accessed using the assays function, described below. This returns a SimpleList-class instance. Each element of the list must itself be a matrix (of any mode) and must have dimensions that are the same as the dimensions of the SummarizedExperiment in which they are stored. Row and column names of each matrix must either be NULL or match those of the SummarizedExperiment during construction. It is convenient for the elements of SimpleList of assays to be named.
SummarizedExperiment是适合于矩阵类似的数据。数据访问使用assays功能，如下所述。这将返回一个SimpleList类的实例。列表中的每个元素本身必须是一个矩阵（任何模式），必须有它们存储SummarizedExperiment尺寸相同的尺寸。每个矩阵的行和列名必须是NULL或匹配SummarizedExperiment施工期间的那些。它方便SimpleList检测被命名的元素。
The SummarizedExperiment class has the following slots; this detail of class structure is not relevant to the user.
SummarizedExperiment类有以下插槽;这一类结构的细节是不相关的用户。
exptData A SimpleList-class instance containing
exptData一个simplelist中含有的类的实例
rowData A GRanges-class instance defining the
rowData一个农庄类的实例定义
colData A DataFrame-class instance describing
colData一个DataFrame类的实例描述
assays A SimpleList-class instance, each element of which is a matrix summarizing data associated with the
assays一个simplelist中的类的实例，其中每个元素的总结与相关的数据是一个矩阵
构造----------Constructor----------
Instances are constructed using the SummarizedExperiment function with arguments outlined above.
使用上述论点SummarizedExperiment函数构造实例。
存取----------Accessors----------
In the following code snippets, x is a SummarizedExperiment instance.
在下面的代码片段，x是SummarizedExperiment实例。
assays(x), assays(x) <- value: Get or set the assays. value is a list or SimpleList, each element of which is a matrix with the same dimensions as
assays(x)，assays(x) <- value：获取或设置的检测。 value是list或SimpleList，其中的每个元素是具有相同的尺寸的矩阵
assay(x, i), assay(x, i) <- value: A convenient alternative (to assays(x)[[i]], assays(x)[[i]] <- value) to get or set the ith (default first) assay element. value must be a matrix of the same dimension as x, and with dimension names NULL or consistent with
assay(x, i)，assay(x, i) <- value：assays(x)[[i]]一个方便的替代品（，assays(x)[[i]] <- value）以获取或设置i次检测（默认）元素。 value必须为x同一维度的矩阵，维度名称NULL或一致
rowData(x), rowData(x) <- value: Get or set the row data. value is a GenomicRanges instance. Row names of value must be NULL or consistent with the existing
rowData(x)，rowData(x) <- value：获取或设置行数据。 value是GenomicRanges实例。排名value必须为NULL，或与现有的一致
colData(x), colData(x) <- value: Get or set the column data. value is a DataFrame instance. Row names of value must be NULL or consistent with the existing
colData(x)，colData(x) <- value：获取或设置列的数据。 value是DataFrame实例。排名value必须为NULL，或与现有的一致
exptData(x), exptData(x) <- value: Get or set the experiment data. value is a list or
exptData(x)，exptData(x) <- value：获取或设置的实验数据。 value是list
dim(x): Get the dimensions (ranges x samples) of the
dim(x)：获取尺寸（范围x样品）
dimnames(x), dimnames(x) <- value: Get or set the dimension names. value is usually a list of length 2, containing elements that are either NULL or vectors of appropriate length for the corresponding dimension. value can be NULL, which removes dimension names. This method implies that rownames, rownames<-, colnames,
dimnames(x)，dimnames(x) <- value：获取或设置维度的名称。 value通常是一个长度为2的列表，包含的元素，要么NULL或相应尺寸的适当长度的向量。 value能NULL，删除维度名称。这种方法意味着rownames，rownames<-，colnames
子集----------Subsetting----------
In the code snippets below, x is a SummarizedExperiment instance.
在下面的代码片段，x是SummarizedExperiment实例。
x[i,j], x[i,j] <- value: Create or replace a subset of x. i, j can be numeric, logical, character, or missing. value must be a SummarizedExperiment instance with dimensions, dimension names, and assay elements consistent with the subset
x[i,j]，x[i,j] <- value：创建或替换了x子集。 ij能numeric，logical，character或missing。 value必须是SummarizedExperiment例如维度，维度名称，检测元素与子集一致
作者（S）----------Author(s)----------
Martin Morgan, <a href="mtmorgan@fhcrc.org">mtmorgan@fhcrc.org</a>
参见----------See Also----------
GRanges, DataFrame, SimpleList,
农庄，DataFrame，simplelist中，
举例----------Examples----------
nrows <- 200; ncols <- 6
counts <- matrix(runif(nrows * ncols, 1, 1e4), nrows)
rowData <- GRanges(rep(c("chr1", "chr2"), c(50, 150)),
IRanges(floor(runif(200, 1e5, 1e6)), width=100),
strand=sample(c("+", "-"), 200, TRUE))
colData <- DataFrame(Treatment=rep(c("ChIP", "Input"), 3),
row.names=LETTERS[1:6])
sset <- SummarizedExperiment(assays=SimpleList(counts=counts),
rowData=rowData, colData=colData)
sset
assays(sset) <- endoapply(assays(sset), asinh)
head(assay(sset))
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注：
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发表于 2012-2-25 19:30:15
