newCountDataSet(DESeq)
newCountDataSet()所属R语言包：DESeq
Create a CountDataSet object
创建CountDataSet对象
译者：生物统计家园网 机器人LoveR
描述----------Description----------
This function creates a CountDataSet object from a matrix or data frame of count data.
这个函数创建矩阵计数资料或数据框从1 CountDataSet对象。
用法----------Usage----------
newCountDataSet(countData, conditions, sizeFactors = NULL, phenoData = NULL, featureData = NULL)
参数----------Arguments----------
参数：countData
A matrix or data frame of count data, i.e., of non-negative integer values. The rows correspond to observations (e.g., number of reads that were assigned to a gene), the columns correspond to samples (or experiments). Note that biological replicates should each get their own column, while the counts of technical replicates (i.e., several sequencing ruins/lanes from the same sample) have to be summed up into a single column.
一个矩阵或数据框计数数据，即非负整数的值。行对应的意见（例如，被分配到一个基因的读取次数），列对应样本（或实验）。请注意，生物复制应该得到自己的专栏中，而复制技术的计数（即几个测序废墟/车道从同一样品）要归纳为一个单一的列。
参数：conditions
A factor of experimental conditions (or treatments, or tissue types, or phenotypes, or the like). The length of the factor has to be equal to the number of columns of the countData matrix, assigning a condition to each sample. If 'conditions' is not a factor, it will be converted to one. Alternatively, you may pass a data frame, that will be placed in pData(cds) as is and can then be used with the modes "pooled" and "blind" in estimateVarianceFunctions and its columns can be refered top in a model formula provided to fitNbinomGLMs.
因素的实验条件（或治疗，或组织类型，或表型，或类似）。因素的长度等于的countData矩阵的列数，每个样品分配条件。如果条件是不是一个因素，它会被转换为一个。另外，您可以通过一个数据框，将放在PDATA（CDS）是模式“汇集”和“盲点”estimateVarianceFunctions可以参考其列的顶端，然后可以使用fitNbinomGLMs提供一个模型公式。
参数：sizeFactors
This argument is deprecated. Do not use it. (Size factors should always be estimated from the data with estimateSizeFactors. If you need to set size factors manually for some reasons, change the pData(cds)$sizeFactor.
这种说法已经过时了。不要使用它。 （大小因素应始终从estimateSizeFactors的数据估计，如果您需要手动设置大小的因素，由于某种原因，改变pData(cds)$sizeFactor。
参数：phenoData
You may pass an AnnotatedDataFrame here to describe the columns of the count matrix. Note that the package always adds two rows (or creates a new AnnotatedDataFrame with only these two rows in case you do not supply one) with names "condition" and "sizeFactor" to store this information.
在这里，你可以传递一个AnnotatedDataFrame描述计数矩阵的列。请注意该软件包总是添加两行（或只有这两个行的情况下，你不提供一个创造一个新AnnotatedDataFrame）名称“条件”和“sizeFactor”来存储这些信息。
参数：featureData
You may pass an AnnotatedDataFrame here to describe the rows of the count matrix. The package will just pass through this information without using it. Note that further columns will be added to feature data later, when estimating dispersions.
在这里，你可以传递一个AnnotatedDataFrame描述计数矩阵的行。通过这个信息包将不使用它。请注意，进一步列将添加到特征数据后，估计分散时。
Details
详情----------Details----------
See also CountDataSet-class and the documentation of eSet (package Biobase) for the meaning of the other slots, which CountDataSet inherits from eSet (but which the present package does not use).
也见CountDataSet-class和eSet（包BIOBASE）文件的其他插槽，哪个CountDataSet继承ESET（但目前包不使用）的含义。
值----------Value----------
an object of class CountDataSet
一个类CountDataSet的对象
作者（S）----------Author(s)----------
Simon Anders, sanders@fs.tum.de
举例----------Examples----------
countsTable <- counts( makeExampleCountDataSet() )
cds <- newCountDataSet( countsTable, c( "A", "A", "A", "B", "B" ) )
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 2012-2-25 16:33:12
