R语言 EDASeq包 SeqExpressionSet-class()函数中文帮助文档(中英文对照)

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SeqExpressionSet-class(EDASeq)
SeqExpressionSet-class()所属R语言包：EDASeq

                                        "SeqExpressionSet" class for collections of short reads
                                         “SeqExpressionSet”短读取集合类

                                         译者：生物统计家园网 机器人LoveR

描述----------Description----------

This class represents a collection of digital expression data (usually counts from RNA-Seq technology) along with sample information.
这个类表示一个数字表达数据采集样本信息（RNA-seq的技术通常是计数）。


类的对象----------Objects from the Class----------

Objects of this class can be created from a call to the newSeqExpressionSet constructor.
这个类的对象，可以创建从一个检测newSeqExpressionSet构造。


延伸----------Extends----------

Class eSet, directly. Class VersionedBiobase, by class eSet, distance 2. Class Versioned, by class eSet, distance 3.
类eSet，直接。类VersionedBiobase类eSet，距离2。类Versioned类eSet，距离3。


插槽----------Slots----------

Inherited from eSet:
继承自eSet




assayData Contains matrices with equal dimensions, and with column number equal to nrow(phenoData).assayData must contain a matrix exprs with rows represening features (e.g., genes) and columns representing samples. The optional matrix offset can be added to represent a normalization offset to be used for differential expression analysis. See the vignette for details.
assayData包含与同等尺寸的矩阵，列数等于nrow(phenoData)assayData必须包含一个矩阵exprs与represening功能（例如，基因）和列代表样本的行 。可选的矩阵offset可以添加到代表偏移归一化差异表达分析。看到细节暗角。




phenoData Sample information. For compatibility with DESeq, there should be at least the column conditions. See eSet for details.
phenoData样品信息。与DESeq兼容性，至少应该有列conditions。看到eSet详情。




featureData Feature information. It is recomended to include at least length and GC-content information. This slot is used for withinLaneNormalization. See eSet for details.
featureData特征的信息。据recomended至少包括长度和GC含量的信息。这个插槽是用来withinLaneNormalization。看到eSet详情。




experimentData See eSet
experimentData见eSet




annotation See eSet
annotation见eSet




protocolData See link{eSet}
protocolData见link{eSet}


方法----------Methods----------

See eSet for inherited methods. Additional methods:
看到eSet继承的方法。其他方法：




exprs signature(object="SeqExpressionSet"): returns the exprs matrix.
exprssignature(object="SeqExpressionSet")：返回exprs矩阵。




exprs<- signature(object = "SeqExpressionSet"): method to replace the exprs matrix.
exprs < - signature(object = "SeqExpressionSet")：exprs矩阵方法来取代。




offst signature(object = "SeqExpressionSet"):  returns the offset matrix.
offstsignature(object = "SeqExpressionSet")：返回offset矩阵。




offst<- signature(object = "SeqExpressionSet"): method to replace the offset slot.
offst < - signature(object = "SeqExpressionSet")：方法来取代offset插槽。




boxplot signature(x = "SeqExpressionSet"): produces a boxplot of the log counts.
盒形图signature(x = "SeqExpressionSet")：产生的log计数的盒形图。




meanVarPlot signature(x = "SeqExpressionSet"): produces a smoothScatter plot of the mean variance relation. See meanVarPlot for details.
meanVarPlotsignature(x = "SeqExpressionSet")生产smoothScatter的均值方差关系图。看到meanVarPlot详情。




biasPlot signature(x = "SeqExpressionSet", y = "character"): produces a plot of the lowess regression of the counts on some covariate of interest (usually GC-content or length). See biasPlot for details.
biasPlotsignature(x = "SeqExpressionSet", y = "character")生产lowess对一些感兴趣的协（通常GC含量或长度）计数的回归图。看到biasPlot详情。




wihtinLaneNormalization signature(x = "SeqExpressionSet", y = "missing"): within lane normalization for GC-content (or other lane specific) bias. See withinLaneNormalization for details.
wihtinLaneNormalizationsignature(x = "SeqExpressionSet", y = "missing")：内车道标准化的GC含量（或其他车道具体）偏差。看到withinLaneNormalization详情。




betweenLaneNormalization signature(x = "SeqExpressionSet"): between lane normalization for sequencing depth and possibly other distributional differences between lanes.  See betweenLaneNormalization for details.
betweenLaneNormalizationsignature(x = "SeqExpressionSet")：测序深度和其他可能的分布差异之间的车道之间的车道标准化。看到betweenLaneNormalization详情。




coerce signature(from = "SeqExpressionSet", to = "CountDataSet"): coercion to DESeq class CountDataSet for compatibility with downstream analysis.
强制signature(from = "SeqExpressionSet", to = "CountDataSet")：强迫DESeq类CountDataSet兼容性下游分析。


作者（S）----------Author(s)----------


Davide Risso &lt;risso.davide@gmail.com&gt;



参见----------See Also----------

eSet, newSeqExpressionSet, biasPlot, withinLaneNormalization, betweenLaneNormalization
eSet，newSeqExpressionSet，biasPlot，withinLaneNormalization，betweenLaneNormalization


举例----------Examples----------



showMethods(class="SeqExpressionSet", where=getNamespace("EDASeq"))

exprs <- matrix(data=0,nrow=100,ncol=4)
for(i in 1:4) {
exprs[,i] <- rpois(100,lambda=50)
}
cond <- c(rep("A",2),rep("B",2))

counts <- newSeqExpressionSet(exprs,phenoData=AnnotatedDataFrame(data.frame(conditions=cond)))

head(exprs(counts))
boxplot(counts,col=as.numeric(pData(counts)[,1])+1)

转载请注明:出自 生物统计家园网(http://www.biostatistic.net)。


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