mergeExpressionSet(MergeMaid)
mergeExpressionSet()所属R语言包：MergeMaid
Class mergeExpressionSet, a class for merged microarray data, and methods for
mergeExpressionSet类，一类为合并后的微阵列数据和方法
译者：生物统计家园网 机器人LoveR
描述----------Description----------
This is class representation for merged Microarray Data.
这是类合并后的微阵列数据的代表性。
Details
详情----------Details----------
The mergeExpressionSet class is conceived as an extension of the ExpressionSet class provided in Biobase for the storage of expression array data. A mergeExpressionSet object is primarily a list of ExpressionSet objects, along with an incidence matrix indicating which genes appear in which studies. A mergeExpressionSet object with a single study reverts to the ExpressionSet class. A number of accessor functions are defiined for this class, as well as a few convenient analysis and plotting functions.
mergeExpressionSet类被看作是表达阵列数据存储在BIOBASE提供ExpressionSet类的扩展。一个mergeExpressionSet对象主要是ExpressionSet对象名单，连同关联矩阵，说明哪些基因研究出现。与一个单一的研究的mergeExpressionSet对象恢复的ExpressionSet类的。存取功能defiined这个类，以及一些方便的分析和绘图功能。
插槽----------Slots----------
We assume there are K studies, representing a total of M unique genes.
我们假设有K的研究，代表了M的独特的基因。
data A list of ExpressionSet objects.
数据列表ExpressionSet对象。
geneStudy Binary incidence matrix with M rows and K columns. Each column represents a study, and each row represents a gene. If study "s" contains gene "g", then geneStudy[g,s]=1, otherwise geneStudy[g,s]=0.
geneStudy二进制矩阵与M行和k列的发病率。每一列代表一个研究，每一行代表一个基因。如果研究的“S”包含基因“克”，然后geneStudy [G] = 1，否则geneStudy [G] = 0。
notes Object of class "character" This slot is available for storage of descriptive information.
票据类“性格”这个插槽的对象是用于描述信息的存储。
方法----------Methods----------
Derived from ExpressionSet:
来自ExpressionSet：
exprs(mergeExpressionSet) An accessor function for the data slot.
exprs（mergeExpressionSet）数据槽的存取功能。
exprs<- (mergeExpressionSet) A replace function for the data slot
exprs < - （mergeExpressionSet）Replace函数的数据槽
notes (mergeExpressionSet) An accessor function for the notes slot.
票据（mergeExpressionSet）票据插槽存取功能。
notes<- (mergeExpressionSet) A replace function for the notes slot.
笔记< - （mergeExpressionSet）票据插槽替换功能。
geneNames (mergeExpressionSet) Accessor function for union of gene ids in all studies.
geneNames（mergeExpressionSet）基因IDS工会存取功能，在所有的研究。
geneNames<- (mergeExpressionSet) A replace function for gene ids.
geneNames < - （mergeExpressionSet）一个替换基因IDS的功能。
Class-specific methods:
类的具体方法：
geneStudy (mergeExpressionSet) Accessor function for the geneStudy slot.
geneStudy（mergeExpressionSet）为geneStudy插槽存取功能。
phenoData (mergeExpressionSet) Accessor function for phenodata in ExpressionSet's. Returns a list, one phenodata matrix per study.
phenoData（mergeExpressionSet）为phenodata的存取功能，在ExpressionSet的。返回一个列表，每一个研究phenodata矩阵。
phenoData<- (mergeExpressionSet) A replace function for phenodata in ExpressionSet's. Returns a list, one phenodata matrix per study.
phenoData < - （mergeExpressionSet）在ExpressionSet的phenodata的替换功能。返回一个列表，每一个研究phenodata矩阵。
intersection (mergeExpressionSet) Represent data for genes common to all studies as a single ExpressionSet object.
路口（mergeExpressionSet）代表共同所有的研究作为单ExpressionSet对象的基因数据。
modelOutcome (mergeExpressionSet) Calculate regression coefficients for each study/gene.
modelOutcome（mergeExpressionSet）计算每个研究/基因的回归系数。
intCor (mergeExpressionSet) Calculate the integrative correlation coefficients for mergeExpressionSet data.
intCor（mergeExpressionSet）计算综合相关系数为mergeExpressionSet数据。
intcorDens (mergeExpressionSet) Plot the distribution of the integrative correlation coefficients and the null distribution obtained by permutation here we use the approximate method to calculate the integrative correlation.
intcorDens（mergeExpressionSet）图一体化的相关系数分布和置换获得空分布在这里，我们使用近似方法计算综合相关。
Standard generic methods:
标准的通用方法：
length (mergeExpressionSet) Function returning the number of studies in the mergeExpressionSet.
长度（mergeExpressionSet）功能在mergeExpressionSet返回的多项研究。
names (mergeExpressionSet) Function returning study names.
名称（mergeExpressionSet）函数返回研究名。
names<- (mergeExpressionSet) A replace function for study names.
名称< - （mergeExpressionSet）Replace函数的一个研究名称。
[ (mergeExpressionSet) A subset operator. Returns a mergeExpressionSet containing a subset of the studies. A mergeExpressionSet with only one study is returned as a single ExpressionSet.
（mergeExpressionSet）子集运算符。返回一个包含一个子集的研究mergeExpressionSet。一个只有一个研究mergeExpressionSet返回作为单一ExpressionSet。
summary (mergeExpressionSet) Obtain the basic information for 'mergeExpressionSet'.
摘要（mergeExpressionSet）获取的mergeExpressionSet的基本信息。
plot (mergeExpressionSet) Draw scatterplots to compare integrative correlations for genes, here we use the approximate method to calculate the integrative correlation.
图（mergeExpressionSet）绘制散点图一体化相关的基因进行比较，这里我们使用近似方法计算综合相关。
参见----------See Also----------
mergeExprs, intCor, modelOutcome, intcorDens,
mergeExprs，intCor，modelOutcome，intcorDens
举例----------Examples----------
if(require(Biobase) & require(MASS)){
data(mergeData)
merged <-mergeExprs(sample1,sample2,sample3)
merged[1:2]
i<-c(1,3)
merged[i]
exprs(merged)
names(merged)<-c("study1","study2","study3")
length(merged)
summary(merged)
plot(merged)
plot(merged[1:2])
intcorDens(merged)
inter <- intersection(merged)
}
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。
注2：由于是机器人自动翻译，难免有不准确之处，使用时仔细对照中、英文内容进行反复理解，可以帮助R语言的学习。
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发表于 2012-2-26 00:40:48
