DEResult(puma)
DEResult()所属R语言包：puma
Class DEResult
类DEResult
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Class to contain and describe results of a differential expression (DE) analysis. The main components are statistic which hold the results of any statistic (e.g. p-values, PPLR values, etc.), and FC which hold the fold changes.
类包含和描述的差异表达（DE）的分析结果。其主要成分是statistic持有任何统计的结果（如p值，PPLR值等），FC举行的fold change。
创建对象----------Creating Objects----------
DEResult objects will generally be created using one of the functions pumaDE, calculateLimma, calculateFC or calculateTtest.
DEResult对象通常会被使用的功能之一，创建pumaDE，calculateLimma，calculateFC或calculateTtest。
Objects can also be created from scratch:
对象也可以从头开始创建：
new("DEResult")
new("DEResult")
new("DEResult", statistic=matrix() , FC=matrix() , statisticDescription="unknown" , DEMethod="unknown" )
new("DEResult", statistic=matrix() , FC=matrix() , statisticDescription="unknown" , DEMethod="unknown" )
插槽----------Slots----------
statistic: Object of class "matrix" holding the statistics returned by the DE method.
statistic：类“矩阵”持有由DE方法返回的统计对象。
FC: Object of class "matrix" holding the fold changes returned by the DE method.
FC：对象类“矩阵”，持有由DE方法返回的fold change。
statisticDescription: A text description of the contents of the statistic slot.
statisticDescription：一个的statistic插槽内容的文字说明。
DEMethod: A string indicating which DE method was used to create the object.
DEMethod：这方法被用来创建对象的一个字符串，指示。
方法----------Methods----------
Class-specific methods.
类的具体方法。
statistic(DEResult), statistic(DEResult,matrix)<- Access and
statistic(DEResult)，statistic(DEResult,matrix)<-访问和
FC(DEResult), FC(DEResult,matrix)<- Access and
FC(DEResult)，FC(DEResult,matrix)<-访问和
statisticDescription(DEResult), statisticDescription(DEResult,character)<- Access and
statisticDescription(DEResult)，statisticDescription(DEResult,character)<-访问和
DEMethod(DEResult), DEMethod(DEResult,character)<- Access and
DEMethod(DEResult)，DEMethod(DEResult,character)<-访问和
pLikeValues(object, contrast=1, direction="either") Access the statistics of an object of class DEResult, converted to "p-like values". If the object holds information on more than one contrast, only the values of the statistic for contrast number contrast are given. Direction can be "either" (meaning we want order genes by probability of being either up- or down-regulated), "up" (meaning we want to order genes by probability of being up-regulated), or "down" (meaning we want to order genes by probability of being down-regulated). "p-like values" are defined as values between 0 and 1, where 0 identifies the highest probability of being differentially expressed, and 1 identifies the lowest probability of being differentially expressed. We use this so that we can easily compare results from methods that provide true p-values (e.g. calculateLimma) and methods methods that do not provide p-values (e.g. pumaDE). For objects created using pumaDE, this returns 1-PPLR if the direction is "up", PPLR if direction is "down", and 1-abs(2*(PPLR-0.5)) if direction is "either". For objects created using calculateLimma or calculateTtest, this returns the p-value if direction is "either", ((p-1 * sign(FC))/2)+ 0.5, if the direction is "up", and ((1-p * sign(FC))/2)+ 0.5 if the direction is "down". For all other methods, this returns the rank of the appropriate statistic, scaled to lie between 0 and 1. contrast will be returned.
pLikeValues(object, contrast=1, direction="either")类的对象的访问统计DEResult，转换为“P-值”。如果对象拥有一个以上的对比度的信息，只有数量对比contrast统计值给出。方向可以“或者”（这意味着我们要为了基因的可能性，无论是向上或向下调节），“向上”（这意味着我们要责令基因上调的概率），或“向下” （这意味着我们要订购的基因通过下调的可能性）。 “P-值”被定义为0和1之间，其中0标识的差异表达，识别差异表达的最低概率的概率最高值。我们使用，这使我们可以很容易地比较的方法，提供真实的p值（例如calculateLimma）和方法不提供P-值的方法的结果（例如pumaDE）。创建对象使用pumaDE，这回报1-PPLR的方向是“向上”，PPLR如果方向是“向下”，1-ABS（2 *（PPLR-0.5）），如果方向是“ ;“。为对象的创建使用calculateLimma或calculateTtest，这个返回的p值，如果方向是“”，（（P-1号（FC））/ 2）+ 0.5，如果方向“上升”，（（1-P *号（FC））/ 2）+ 0.5，如果方向是“向下”。对于所有其他的方法，此方法返回缩放到介于0和1，适当的统计排名。 contrast将被退回。
topGenes(object, numberOfGenes=1, contrast=1, direction="either") Returns the index numbers (row numbers) of the genes determined to be most likely to be differentially expressed. numberOfGenes specifies the number of genes to be returned by the function. If the object holds information on more than one contrast, only the values of the statistic for contrast number contrast are given. Direction can be "either" (meaning we want order genes by probability of being either up- or down-regulated), "up" (meaning we want to order genes by probability of being up-ragulated), or "down" (meaning we want to order genes by probability of being down-regulated). Note that genes are ordered by "p-like values" (see pLikeValues). object is an object of class DEResult.
topGenes(object, numberOfGenes=1, contrast=1, direction="either")返回的决心是最有可能的差异表达的基因指数（行号）。 numberOfGenes指定由函数返回的基因数量。如果对象拥有一个以上的对比度的信息，只有数量对比contrast统计值给出。方向可以“或者”（这意味着我们要为了基因的可能性，无论是向上或向下调节），“向上”（这意味着我们要订购是，ragulated的概率基因），或“向下” （这意味着我们要订购的基因通过下调的可能性）。请注意，基因是由“P-值”命令（见pLikeValues）。 object类DEResult是一个对象。
topGeneIDs(object, numberOfGenes=1, contrast=1, direction="either") Returns the Affy IDs (row names) of the genes determined to be most likely to be differentially expressed. numberOfGenes specifies the number of genes to be returned by the function. If the object holds information on more than one contrast, only the values of the statistic for contrast number contrast are given. Direction can be "either" (meaning we want order genes by probability of being either up- or down-regulated), "up" (meaning we want to order genes by probability of being up-ragulated), or "down" (meaning we want to order genes by probability of being down-regulated). Note that genes are ordered by "p-like values" (see pLikeValues). object is an object of class DEResult.
topGeneIDs(object, numberOfGenes=1, contrast=1, direction="either")返回Affy决心是最有可能的差异表达的基因标识（列名）。 numberOfGenes指定由函数返回的基因数量。如果对象拥有一个以上的对比度的信息，只有数量对比contrast统计值给出。方向可以“或者”（这意味着我们要为了基因的可能性，无论是向上或向下调节），“向上”（这意味着我们要订购是，ragulated的概率基因），或“向下” （这意味着我们要订购的基因通过下调的可能性）。请注意，基因是由“P-值”命令（见pLikeValues）。 object类DEResult是一个对象。
numberOfProbesets(object) Returns the number of probesets (number of rows) in an object of class DEResult. This method is synonymous with numberOfGenes.
numberOfProbesets(object)返回一个对象类DEResult的probesets的数量（行数）。这种方法是与numberOfGenes的代名词。
numberOfGenes(object) Returns the number of probesets (number of rows) in an object of class DEResult. This method is synonymous with numberOfProbesets.
numberOfGenes(object)返回一个对象类DEResult的probesets的数量（行数）。这种方法是与numberOfProbesets的代名词。
numberOfContrasts(object) Returns the number of contrasts (number of columns) in an object of class DEResult.
numberOfContrasts(object)返回一个对象类DEResult对比数（列数）。
write.reslts(object) signature(x = "DEResult"): writes the statistics and related fold changes (FCs) to files. It takes the same arguments as write.table. The argument "file" does not need to set any extension. The different file marks and extension "csv" will be added automatically. The default file name is "tmp". In the final results, statistics are in the file "tmp\_statistics.csv", and FCs are in
write.reslts(object)signature(x = "DEResult")：写的统计数据及相关倍的变化（FCS）的文件。它需要write.table相同的论点。 “文件”的说法并不需要设置任何扩展。不同的文件标记和扩展“CSV”将被自动添加。默认的文件名是“tmp”的。在最后的结果，统计文件“TMP \ _statistics.csv”，功能界别是在
Standard generic methods:
标准的通用方法：
show(object) Informatively display object contents.
show(object)请提供知识显示对象内容。
作者（S）----------Author(s)----------
Richard D. Pearson
参见----------See Also----------
Related methods pumaDE, calculateLimma, calculateFC or calculateTtest.
相关的方法pumaDE，calculateLimma，calculateFC或calculateTtest。
举例----------Examples----------
## Create an example DEResult object[＃创建一个例子DEResult对象。]
# Next 4 lines commented out to save time in package checks, and saved version used[接下来的4行注释掉包检查，以节省时间，并保存版本使用]
# if (require(affydata)) {[（要求（affydata））{]
# data(Dilution)[数据（稀释）]
# eset_mmgmos <- mmgmos(Dilution)[< - mmgmos eset_mmgmos（稀释）]
# }[}]
data(eset_mmgmos)
# Next line used so eset_mmgmos only has information about the liver factor[下一行使用，所以eset_mmgmos只有肝因子的信息]
# The scanner factor will thus be ignored, and the two arrays of each level[扫描器的因素将被忽略，每个级别的两个数组]
# of the liver factor will be treated as replicates[肝因子，将被视为重复]
pData(eset_mmgmos) <- pData(eset_mmgmos)[,1,drop=FALSE]
# To save time we'll just use 100 probe sets for the example[为了节省时间，我们只使用100个探针组的例子]
eset_mmgmos_100 <- eset_mmgmos[1:100,]
eset_comb <- pumaComb(eset_mmgmos_100)
esetDE <- pumaDE(eset_comb)
## Use some of the methods[＃使用的一些方法]
statisticDescription(esetDE)
DEMethod(esetDE)
numberOfProbesets(esetDE)
numberOfContrasts(esetDE)
topGenes(esetDE)
topGenes(esetDE, 3)
pLikeValues(esetDE)[topGenes(esetDE,3)]
topGeneIDs(esetDE, 3)
topGeneIDs(esetDE, 3, direction="down")
## save the expression results into files[＃表达的结果保存到文件]
write.reslts(esetDE, file="example")
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。
注3：如遇到不准确之处，请在本贴的后面进行回帖，我们会逐渐进行修订。
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发表于 2012-2-26 11:33:18
