cellHTS-class(cellHTS2)
cellHTS-class()所属R语言包：cellHTS2
A class for data from cell-based high-throughput assays
A类为基于单元的高通量的检测数据
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Container for data and experimental meta-data from cell-based high-throughput assays performed in plate format. Typical applications are RNA interference or small molecular compound screens. The class extends the NChannelSet class. Data are from experiments where the same set of reagents (probes) where used. The class can represent data from multi-channel assays.
数据和实验，从单元为基础的高通量检测板格式进行元数据的容器。典型的应用是RNA干扰或小分子化合物的屏幕。类扩展NChannelSet类。数据是从实验试剂的同一组（探针）使用。类可以代表从多渠道的检测数据。
The data can be thought of as being organised in a two- or three-dimensional array as follows:
数据可以被认为是作为在两个或三维数组安排如下：
The first dimension corresponds to reagents (e.g. siRNAs, chemical compounds) that were used in the assays. For example, if the screen used 100 plates of 384 wells (24 columns, 16 rows), then the first dimension has size 38,400, and the cellHTS object keeps track of plate ID, row, and column associated with each element. For historic reasons, and because we are using infrastructure that was developed for microarray experiments, the following terms are used synonymously for the elements of the first dimension: reagents, features, probes, genes.
第一维对应，在实验中使用的试剂（如siRNAs的化合物）。例如，如果在屏幕上用100板384井（24列，16行），然后第一维的大小是38,400，对象保持cellHTS板ID的轨道，行和列与每个元素相关。由于历史原因，因为我们使用微阵列实验开发的基础设施，以下条款使用的第一维的元素：试剂，功能，探针，基因的同义词。
The second dimension corresponds to assays, including replicates and different experimental conditions (cell type, treatment, genetic background). A potentially confusing terminology is that the data structure that annotates the second dimension is called phenoData. This is because we are using infrastructure (the NChannelSet class) that uses this unfortunate term for this purpose. The software provides methodology for replicate summarization and scoring, however more complicated experimental designs are not directly supported. Multi-purpose tools like lmFit in the limma package should be consulted.
第二维对应分析，包括复制和不同的实验条件（单元类型，治疗，遗传背景）。一个潜在的混淆的术语，诠释了第二个维度的数据结构被称为phenoData。这是因为我们正在使用的基础设施（NChannelSet类），为此这个不幸的术语使用。该软件提供了复制的总结和评分方法，但是更复杂的实验设计不直接支持。多用途的工具，如lmFitlimma包应谘询。
The (optional) third dimension corresponds to different channels (e.g. different luminescence reporters)
（可选的）第三个维度对应不同的渠道（例如，不同的发光记者）
类的对象----------Objects from the Class----------
Objects can be created by calls of the form new("cellHTS", assayData, phenoData, ...). See the examples below.
创建对象可以通过检测的形式new("cellHTS", assayData, phenoData, ...)。见下面的例子。
插槽----------Slots----------
plateList: a data.frame containing what was read from input measurement data files plus a column status of type character containing the string "OK" if the data import appeared to have gone well, and the respective error
plateList：data.frame包含了从输入测量数据文件中读取加列status类型的字符，包含字符串“OK”，如果数据导入出现已顺利各自的错误
intensityFiles: a list, where each component contains a copy of the imported input data files. Its length corresponds to
intensityFiles：一个列表，其中每个组件包含进口的输入数据文件副本。它的长度相当于
state: a logical vector of length 4 representing the processing status of the object. It must have the names
state：逻辑向量的长度为4，代表该对象的处理状态。它必须有名称
plateConf: a data.frame containing what was read from the configuration file for the experiment (except the first two header rows). It contains at least three columns named Plate, Well and Content. Columns Plate and Well are allowed to contain
plateConf：data.frame包含了从实验的配置文件（除前两个标题行）读取。它包含至少三列名为Plate，Well和Content。列Plate和Well允许包含
screenLog: a data.frame containing what was read from the screen log file for the experiment, in case it exists. Contains at least three columns, and column names Plate, Well, and Flag. Additional columns are Sample (when there are replicates or more than one sample or condition) and Channel (when there are multiple
screenLog：data.frame读实验，从屏幕上的log文件的情况下存在。包含至少三列，列名Plate，Well，Flag。附加列Sample（当有复制或一个以上的样品或条件）和Channel（当有多个
screenDesc: a character containing what was read from
screenDesc：是读取字符
rowcol.effects: a 3D array of size Features (i.e. plate size x number of plates) x Samples x Channels
rowcol.effects：三维数组的大小特点（即板尺寸板的数量x）x样品的X通道
overall.effects: a 3D array of size Features x
overall.effects：大小特征的三维数组x
assayData: Object of class AssayData, usually an environment containing matrices of identical size. Each matrix represents a single channel. Columns in each matrix correspond to samples (or replicate), rows to features (probes). Once created,
assayData：Object类的AssayData，通常含有相同大小的矩阵环境。每个矩阵代表一个通道。每个矩阵中的列对应的样本（或复制），行功能（探针）。一旦创建，
plateData: A list of data frames, with number of rows of each frame equal to the number of plates used in the assay and number of columns equal to the number of samples. Each data frame in the list should contain factorial annotation information relevant for the individual plates, like experimental batches or varying types of micro-titre plates. Currently, this information will be used for between-batch normalization and quality
plateData：一个数据框的名单与板使用的检测样本数等于列数等于每帧的行数。列表中的每个数据框应包含阶乘的注释信息有关的个别板块，像实验批次或不同类型的微滴度板。目前，这些信息将用于批次之间的标准化和质量
phenoData: Object of class AnnotatedDataFrame. Please see the documentation of the phenoData slot of NChannelSet for more details.
phenoData类AnnotatedDataFrame的对象。请看到phenoData插槽NChannelSet更多细节的文档。
It contains information about the screens, and it must have the following columns in its data component: replicate and assay, where replicate is expected to be a vector of integers giving the replicate number, while assay is expected to be a vector of characters giving the name of the biological assay. Both of these vectors should have the same length as the number of Samples.
它包含有关屏幕的信息，它必须在其data组件有以下几列：replicate和assay，其中replicate预计是给一个整数向量复制的数量，而assay预计将给人的生物实验的名称的字符向量。这些向量都应该有相同长度的样本数量。
Once created, cellHTS coordinates selection and subsetting
一旦创建，cellHTS坐标选择和子集
featureData: Object of class AnnotatedDataFrame, containing information about the reagents: plate, well, column, the well annotation (sample, control, etc.), etc. For a cellHTS object, this slot must contain in its data component at least three mandatory columns named plate, well and controlStatus. Column plate is expected to be a numeric vector giving the plate number (e.g. 1, 2, ...), well should be a vector of characters (alphanumeric characters) giving the well ID within the plate (e.g. A01, B01, H12, etc.). Column controlStatus should be a factor specifying the annotation for each well with possible levels: empty, other, neg, sample, and pos. Other levels besides pos and
featureData类AnnotatedDataFrame，其中包含的信息对试剂的对象：好，板，柱的，以及注释（样品，控制等）等，对于一个cellHTS对象，这个插槽必须包含至少有三个强制性列名为data，plate和wellcontrolStatus组件。 plate预计将提供车牌号码（例如：1，2，...）数字矢量列，well应该是一个矢量字符（字母数字字符），以及身份证内盘（例如的A01，B01，H12，等）。列controlStatus应该是一个因素，指定每口井可能层次的注解：空的，其他的，NEG，样本，和POS。除了POS和其他各级
experimentData: Object of class MIAME containing descriptions
experimentData类MIAME包含描述：对象
annotation: A "character" of length 1, which can be used to specify the name of an annotation package that goes
annotation："character"长度为1，可用于指定一个注解包云的名字
processingInfo: A list containing information about
processingInfo：一个列表，其中包含的信息
.__classVersion__: Object of class Versions, containing automatically created information about the class definition, Biobase package version, and other information about the user system at the time the instance was created. See classVersion and
.__classVersion__：Object类的Versions，包含自动创建的类的定义，BIOBASE包的版本，并在创建实例时用户系统的其他信息的信息。看到classVersion“
延伸----------Extends----------
Class NChannelSet, directly.
类NChannelSet，直接。
方法----------Methods----------
Methods with class-specific functionality:
类特定功能的方法：
name(object) signature(object="cellHTS"). Obtains the name of the assay stored in the object. This corresponds to the contents of column assay of the
name(object)signature(object="cellHTS")。获取存储在object该法的名称。这对应列的assay的内容
name(object) <- value signature(object = "cellHTS", value = "character") assign the character of length one (value) to the elements in column assay of the
name(object) <- valuesignature(object = "cellHTS", value = "character")列value分配字符元素的长度为一（assay）
signature(object = "cellHTS"). Obtain the plate dimension for the data stored in object.
signature(object = "cellHTS")。获得的数据存储在object板尺寸。
signature(object = "cellHTS", value = "character"). Replace the channel names in object.
signature(object = "cellHTS", value = "character")。更换object频道名称。
signature(object = "cellHTS"). Obtain the total number of batches for the data stored in object.
signature(object = "cellHTS")。获得为object中存储的数据的批次总数。
compare2cellHTS(x, y) signature(x = "cellHTS", y = "cellHTS"). Compares two cellHTS objects, x and y, returning TRUE if they are from the same experiment (i.e. if they derive from the same
compare2cellHTS(x, y)signature(x = "cellHTS", y = "cellHTS")。比较两个cellHTS对象，x和y回TRUE如果他们是相同的实验（即如果他们从同一
Methods with functionality derived from class NChannelSet: channel, channelNames, selectChannels, object[features, samples], sampleNames
与功能的方法来源于类NChannelSet：channel，channelNames，selectChannels，object[features, samples]，sampleNames
Methods with functionality derived from eSet: annotation, assayData, assayData<-, classVersion, classVersion<-, dim, dims, experimentData, featureData, phenoData, phenoData<-, pubMedIds, sampleNames, sampleNames<-, storageMode, varMetadata, isCurrent, isVersioned.
eSet，annotation，assayData，assayData<-，classVersion，classVersion<-，<X：dim派生功能的方法>，dims，experimentData，featureData，phenoData，phenoData<-，pubMedIds，sampleNames，sampleNames<- storageMode，varMetadata，isCurrent。
Additional methods:
其他方法：
initialize used internally for creating objects
initialize用于内部创建对象
show invoked automatically when the object is
show时会自动调用对象是
state Access the state slot of a
state进入state插槽
annotate Annotate the cellHTS
annotate批注cellHTS
configure Configure the cellHTS object using the the screen description file, the
configure配置cellHTS对象使用的屏幕描述文件，
writeTab Write the contents of assayData slot
writeTabassayData槽的内容写入
ROC Construct an object of S4 class ROC, which represents a receiver-operator-characteristic curve, from the data of the annotated positive and negative controls in a scored
ROCS4类ROC，它代表一个接收操作特性曲线，在刻痕注明的阳性和阴性对照的数据，构造一个对象
meanSdPlot(x) signature(x = "cellHTS") plots row standard deviations across samples versus row means across samples for data stored in slot assayData of a cellHTS object. If there are multiple channels, row standard deviations and row means are calculated across samples for each channel separately. Only wells containing "sample" are considered. See meanSdPlot for more details
meanSdPlot(x)signature(x = "cellHTS")图划船横跨样品与样品之间的行手段插槽assayDatacellHTS对象中存储的数据的标准偏差。如果有多种渠道，行的标准偏差和行手段在每个通道的样本分别计算。被认为只包含“样本”的井。 meanSdPlot更多细节
作者（S）----------Author(s)----------
Ligia P. Bras <a href="mailto:ligia@ebi.ac.uk">ligia@ebi.ac.uk</a>, Wolfgang Huber <a href="mailto:huber@ebi.ac.uk">huber@ebi.ac.uk</a>
参见----------See Also----------
NChannelSet readPlateList annotate configure writeTab state Data normalizePlates ROC
NChannelSetreadPlateListannotateconfigurewriteTabstateDatanormalizePlatesROC
举例----------Examples----------
showClass("cellHTS")
showMethods(class="cellHTS")
## An empty cellHTS[＃空cellHTS，]
obj <- new("cellHTS")
data("KcViabSmall")
KcViabSmall
state(KcViabSmall)
## Replicate 1 as a cellHTS object[＃复制作为cellHTS对象1]
y <- KcViabSmall[,1]
compare2cellHTS(KcViabSmall, y)
data("KcViab")
compare2cellHTS(KcViab, KcViabSmall)
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。
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发表于 2012-2-25 14:14:14
