cellHTS2(cellHTS2)
cellHTS2()所属R语言包：cellHTS2
cellHTS2 Package Overview
cellHTS2包装概述
译者：生物统计家园网 机器人LoveR
描述----------Description----------
cellHTS2 Package Overview
cellHTS2包装概述
Details
详情----------Details----------
This package provides data structures and algorithms for cell-based high-throughput assays performed in plate format. Typical applications are RNA interference or small molecular compound screens. The most important data class is cellHTS, which extends the NChannelSet class.
这个包提供了用于基于单元的高通量板格式进行分析的数据结构和算法。典型的应用是RNA干扰或小分子化合物的屏幕。最重要的数据类是cellHTS，延伸NChannelSet类的。
Full help on methods and associated functions is available from within class help pages.
从帮助页面内类，方法和相关职能的充分帮助。
Data sets: KcViab, KcViabSmall, oldKcViabSmall, dualCh, bdgpbiomart.
数据集：KcViab，KcViabSmall，oldKcViabSmall，dualCh，bdgpbiomart。
Introductory information is available from vignettes, type openVignette().
介绍信息是从短文，键入openVignette()。
Class-specific methods: annotate, batch, batch<-, compare2cellHTS, configure, Data, Data<-, geneAnno, intensityFiles, name, name<-, nbatch, pdim, plate, plateConf, plateEffects, plateList, position, screenDesc, screenLog, state, well, wellAnno, writeTab, ROC.
类的具体方法：annotate，batch，batch<-，compare2cellHTS，configure，Data，Data<-，<X >，geneAnno，intensityFiles，name，name<-，nbatch，pdim，plate，plateConf plateEffects，plateList，position，screenDesc，screenLog，state，well，wellAnno， writeTab。
Generic functions: show, initialize, validObject.
通用功能：show，initialize，validObject。
Other functions: oneRowPerId, write.tabdel, readPlateList, readHTAnalystData, normalizePlates, Bscore, spatialNormalization, plotSpatialEffects, summarizeChannels, scoreReplicates, summarizeReplicates, imageScreen, configurationAsScreenPlot, getEnVisionRawData, getEnVisionCrosstalkCorrectedData, getTopTable, getMeasureRepAgreement. getDynamicRange, getZfactor, writeReport, convertOldCellHTS, scores2calls, and templateDescriptionFile.
其他功能：oneRowPerId，write.tabdel，readPlateList，readHTAnalystData，normalizePlates，Bscore，spatialNormalization，plotSpatialEffects summarizeChannels，scoreReplicates，summarizeReplicates，imageScreen，configurationAsScreenPlot，getEnVisionRawData，getEnVisionCrosstalkCorrectedData，getTopTable， getMeasureRepAgreement。 getDynamicRange，getZfactor，writeReport，convertOldCellHTS，scores2calls，templateDescriptionFile。
A full listing of documented topics is available in HTML view by typing help.start() and selecting the cellHTS2 package from the Packages menu or via library(help="cellHTS2").
键入help.start()和选择cellHTS2菜单或通过Packages的library(help="cellHTS2")包的记录主题的完整列表可在HTML视图。
作者（S）----------Author(s)----------
Ligia P. Bras
参考文献----------References----------
Analysis of cell-based RNAi screens, Genome Biology 7, R66.
参见----------See Also----------
Below, we present a list of "high level" functions in the celHTS2 package together with a brief description of what they do.
下面，我们提出的“高层次”的功能的简要介绍，他们做了什么在celHTS2封装与列表。
Data import:
数据导入：
readPlateList read a collection of plate reader data files.
readPlateList读酶标仪数据文件的集合。
readHTAnalystData read input files from a HTanalyser plate reader containing data for a set of plate replicates.
readHTAnalystData从HTanalyser板读者的板集复制的数据读取输入文件。
getEnVisionRawData this function can be used as an import function when calling readPlateList to read plate result files obtained from EnVision Plate Reader.
getEnVisionRawData这个函数可以作为进口函数调用readPlateListenVision的微孔板读板结果获得的文件时使用。
getEnVisionCrosstalkCorrectedData this function can be used as an import function when calling readPlateList to read plate result files obtained from EnVision Plate Reader.
getEnVisionCrosstalkCorrectedData这个函数可以作为进口函数调用readPlateListenVision的微孔板读板结果获得的文件时使用。
Screen configuration and annotation:
屏幕配置和注释：
annotate annotates the reagents (e.g. siRNAs, molecular compounds) of a cellHTS object.
annotate诠释cellHTS对象的试剂（如siRNA的分子化合物）。
configure annotates the plates and the plate result files of a gcellHTS object.
configure诠释AGcellHTS对象的板和板结果文件。
Accessors:
存取：
batch accesses and replaces the batch slot of a cellHTS object.
batch访问，并取代batch一个cellHTS对象插槽。
Data accesses and replaces the assayData slot of a cellHTS object. It returns a 3D array with dimensions number of features (product between the number of wells per plates and the number of plates) x number of samples (or replicates) x number of channels.
Data访问，并取代assayData一个cellHTS对象插槽。它返回一个三维数组的维数功能（井每板数量和板之间的产品）样本数（或复制）×渠道。
geneAnno returns the reagent IDs used in the screen (i.e. the contents of fData(object)[,"GeneID"].
geneAnno返回在屏幕上使用的试剂ID（即fData(object)[,"GeneID"]的内容。
intensityFiles returns a list, where each component contains a copy of the imported input data files.
intensityFiles返回一个列表，其中每个组件包含进口输入的数据文件的副本。
name obtains the name(s) of the assay, or multiple assays, stored in the object. This corresponds to the contents of column assay of the phenoData slot of the cellHTS object.
name获得该法的名称（S），或多个检测，储存在object。这对应栏的内容assayphenoDatacellHTS对象插槽。
pdim obtains the plate dimensions (number of rows and columns) for the data stored in object.
pdim得到的数据存储在object板尺寸（行数和列数）。
plate plate identifier for each feature (well).
plate每个功能板标识符（井）。
plateConf returns a data.frame that contains what was read from the plate configuration input file (except the first two header rows) during the screen configuration step.
plateConf返回包含在屏幕的配置步骤是从板块配置的输入文件（除前两个标题行）读取数据框。
plateList returns a data.frame containing what was read from the plate list file, plus a column status of type character that contains the string "OK" if the data import appeared to have gone well, and the respective error or warning message otherwise.
plateList返回一个数据框包含了什么板列表文件读取，加上一列status类型的字符，其中包含字符串“OK”，如果数据导入出现已顺利各自的错误或警告消息，否则。
plateEffects accesses the slots rowcol.effects and overall.effects.
plateEffects访问的插槽rowcol.effects和overall.effects。
position gives the well number for each feature (well) within each plate.
position给每个功能（井）以及每块板内。
screenDesc returns an object of class character that contains what was read from the screen description input file during the configuration of the cellHTS object.
screenDesc返回一个类的对象character，它包含了从屏幕上的说明输入文件读期间cellHTS对象的配置。
screenLog returns a data.frame containing what was read from the screen log input file during the screen configuration step.
screenLog返回一个数据框包含在屏幕的配置步骤是从屏幕log输入文件读。
state This generic function accesses the state of an object derived from the cellHTS class.
state这个泛型函数访问cellHTS类派生的对象的状态。
well gives the alphanumeric identifier (e.g. A01, A02, ...) for each well and plate.
well给每口井和板的字母数字标识符（如A01，A02，...）。
wellAnno accesses the plate annotation stored in fData(object)[,"controlStatus"].
wellAnno访问存储板fData(object)[,"controlStatus"]注释。
Data preprocessing:
数据预处理：
All the following methods work on the data stored in the slot assayData of a cellHTS object.
所有下列方法工作对插槽assayDatacellHTS对象中存储的数据。
normalizePlates per-plate data transformation, normalization and variance adjustment.
normalizePlates每盘数据转换，规范化和方差调整。
Bscore correction of plate and spatial effects using the B score method (without variance adjustment of the residuals).
Bscore校正板和使用方法（无残差的方差调整）的B得分的空间效果。
spatialNormalization correction of spatial effects by fitting a polynomial surface within each plate using local regression (loess or robust local fit). Uses a second degree polynomial (local quadratic fit). Only wells containing "sample" are considered to fit the models.
spatialNormalization校正在每个板采用局部回归拟合一个多项式曲面（loess或robust local fit）的空间效果。使用第二个多项式（局部二次拟合）。只包含“样本”的井被认为是适合的模型。
summarizeChannels combines intensities from a dual-channel assay by applying the function defined in fun.
summarizeChannels应用fun定义的函数，结合双通道检测强度。
scoreReplicates transform per-replicate values into scores.
scoreReplicates每重复值转化成分数。
summarizeReplicates summarizes between normalized and scored replicate values, obtaining a single value for each probe.
summarizeReplicates总结规范化，并取得复制值之间，获得每个探针的单值。
scores2calls applies a sigmoidal transformation to the z-score values stored in a cellHTS object mapping them to the range [0,1].
scores2calls适用于S型转化为Z-得分值存储在一个cellHTS对象的范围内将它们映射到[0,1]。
Miscellaneous:
杂项：
compare2cellHTS compares two cellHTS objects to see whether they derive from the same initial cellHTS object.
compare2cellHTS比较两个cellHTS对象，看他们是否获得相同的初始cellHTS对象。
convertOldCellHTS converts an old S3 class cellHTS object obtained using cellHTS package to new S4 class cellHTS object(s) to use with package cellHTS2.
convertOldCellHTS转换旧的S3类cellHTS对象获得新的S4类使用cellHTS包包cellHTS使用cellHTS2对象（S）。
convertWellCoordinates converts between different ways of specifying well coordinates within a plate. For example, wells can be identified by an alphanumeric character (e.g. "B02" or c("B", "02")) or by an integer value (e.g. 26).
convertWellCoordinates之间不同的方式指定一个板块内以及坐标转换。例如，水井可以识别字母数字字符（如“B02”或“B”C（“02”）），或由一个整数（例如26）。
ROC creates an object of class ROC from a scored cellHTS object which can be plotted as a ROC curve.
ROC创建一个类的对象ROC1拿下cellHTS对象可以作为ROC曲线绘制。
getTopTable generates the hit list from a scored cellHTS object and write it to a tab-delimited file.
getTopTable产生1刻痕cellHTS对象的暗杀名单，并将其写入到一个制表符分隔的文件中。
getMeasureRepAgreement calculates the agreement between plate replicates using raw data or normalized data stored in a cellHTS object.
getMeasureRepAgreement计算板之间的协议，重复使用原始数据或规范化的数据存储在cellHTS对象。
getDynamicRange calculates per-plate dynamic range of data stored in a cellHTS object.
getDynamicRangecellHTS对象中存储的数据计算每盘动态范围。
getZfactor calculates per-experiment Z'-factor of data stored in a cellHTS object. The Z'-factor is a measure that quantifies the separation between the distribution of positive and negative controls.
getZfactor计算每个实验Z因素cellHTS对象中存储的数据。 Z的因素是一个措施，量化阳性和阴性对照的分布之间的分离。
plotSpatialEffects this function plots the per-plate row and column effects estimated by the B score method or by the spatial normalization.
plotSpatialEffects这个功能图板每行和列的影响估计由B评分方法或空间标准化。
imageScreen creates an image plot that gives an overview of the whole set of score values stored in a scored cellHTS object.
imageScreen创建了一个形象的图，给出了一个概述1拿下cellHTS对象中的一组存储的整个分值。
writeReport creates a directory with HTML pages of linked tables and plots documenting the contents of the preprocessing of a cellHTS object.
writeReport目录创建HTML页面记录cellHTS对象的预处理内容的链接表和图。
oneRowPerId rearranges dataframe entries such that there is exactly one row per ID.
oneRowPerId重新排列dataframe条目，每个ID恰好有一个行。
nbatch gives the total number of batches in a cellHTS object.
nbatch给cellHTS对象的批次总数。
templateDescriptionFile creates a template description file for an RNAi experiment with default entries compliant with MIAME class and with additional entries specific for a cellHTS object.
templateDescriptionFile创建一个RNAi实验模板默认条目符合MIAME类的和额外的条目与cellHTS对象的具体描述文件。
writeTab this function is a wrapper for the function write.table to write the contents of assayData slot of a cellHTS object to a tab-delimited file. If the object is already annotated, the probe information (fData(object)@GeneID) is also added.
writeTab这个函数是一个函数的包装write.table写assayDatacellHTS对象制表符分隔的文件插槽的内容。“如果对象是已经注明，探针信息（fData(object)@GeneID）也增加了。
write.tabdel a wrapper for the function write.table used to write data to a tab-delimited file.
write.tabdel函数的包装write.table使用制表符分隔的文件中写入数据。
meanSdPlot method for meanSdPlot (from the vsn package) to construct the standard deviation versus mean plot of data stored in a cellHTS object.
meanSdPlotmeanSdPlot（vsn包）建设的标准差与平均图cellHTS对象中存储的数据的方法。
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 14:14:30
