PREDADataAndResults-class(PREDA)
PREDADataAndResults-class()所属R语言包：PREDA
Class "PREDADataAndResults" is used to manage the PREDA analysis output
用于类“PREDADataAndResults”管理普雷达分析输出
译者：生物统计家园网 机器人LoveR
描述----------Description----------
This class is used to manage the PREDA analysis output along with corresponding input data
这个类是用来管理普雷达分析输出相应的输入数据
类的对象----------Objects from the Class----------
Objects can be created by calls of the form new("PREDADataAndResults", ids, chr, start, end, strand, chromosomesNumbers, chromosomesLabels, position, optionalAnnotations, optionalAnnotationsHeaders, analysesNames, testedTail, smoothStatistic, pvalue, qvalue, statistic).
创建对象可以通过检测的形式new("PREDADataAndResults", ids, chr, start, end, strand, chromosomesNumbers, chromosomesLabels, position, optionalAnnotations, optionalAnnotationsHeaders, analysesNames, testedTail, smoothStatistic, pvalue, qvalue, statistic)。
插槽----------Slots----------
analysesNames: Object of class "character" a character vector of unique names associated to each column of smoothStatistic, pvalue and qvalue matrices.
analysesNames类"character"相关每个smoothStatistic列的唯一的名称的字符向量，pvalue和qvalue矩阵的对象。
testedTail: Object of class "character" a character describing what tail of the statistic distribution will be analyzed during PREDA analysis.
testedTail：Object类的"character"字符描述普雷达分析分析什么样的统计分布的尾部将在。
smoothStatistic: Object of class "matrix" a numeric matrix containing smoothed observed statistics as obtained from PREDA analysis. The smoothed statistics must be provided as a matrix of numeric values, with a number of rows equal to the length of "ids" slot and a number of columns equal
smoothStatistic：Object类的"matrix"数字矩阵包含平滑普雷达分析获得的观察统计。平滑的统计数据，必须提供一个数值矩阵，与行数等于“IDS”槽的长度和列数相等
pvalue: Object of class "matrix" a numeric matrix containing unadjusted gene-centered pvalues as obtained from PREDA analysis. The pvalue matrix must be provided as a matrix of numeric values, with a number of rows equal to the length of "ids" slot and a number of columns equal
pvalue：Object类的"matrix"普雷达分析得到的pvalues未经调整以基因为中心的数字矩阵。必须提供一个数值矩阵，pvalue矩阵的行数等于“IDS”槽的长度和列数相等
qvalue: Object of class "matrix" a numeric matrix containing adjusted gene-centered pvalues as obtained from PREDA analysis: i.e. usually FDR adjusted pvalues, but other multiple testing methods could be adopted as well The qvalue matrix must be provided as a matrix of numeric values, with a number of rows equal to the length of "ids" slot and a number of columns equal
qvalue：Object类的"matrix"以及通过数字矩阵，包含调整为中心的基因pvalues普雷达分析得到：即通常FDR校正pvalues的，但其他多个测试方法可以qvalue矩阵必须作为一个数值矩阵，提供了“IDS”槽的长度等于行和列数相等数量
position: Object of class "integer" a numeric vector of reference genomic positions that will be associated and used for each genomic feature under investigation for smoothing data during PREDA analysis.
position：Object类的"integer"将相关的基因和基因组功能为每个正在调查平滑在普雷达分析数据使用参考位置的数字矢量。
ids: Object of class "character" a character vector of unique identifiers for the genomic features under investigation
ids：对象类的"character"正在调查中的基因组功能的唯一标识符的字符向量
chr: Object of class "integer" a numeric vector representing the chromosome where each ids is mapped. Please note that chromosome usually not represented with a number must will be comverted to a number as well. e.g. for Human, chromsomomees X and Y will be converted to chromsomes 23 and 24 respectively.
chr：Object类的"integer"一个数字代表ID的映射，其中每个染色体的向量。请注意，染色体通常不能代表一个数字，必须将comverted数字。例如人权，chromsomomees X和Y将被转换为chromsomes 23日和24日分别。
start: Object of class "integer" a numeric vector of start genomic position for each genomic feature under investigation (i.e. gene, transcript, SNP or other elements).
start：Object类的"integer"一开始正在调查中的每个基因的功能（即基因的转录，SNP或其他元素）的基因组位置的数字向量。
end: Object of class "integer" a numeric vector of end genomic position for each genomic feature under investigation (i.e. gene, transcript, SNP or other elements).
end：Object类的"integer"正在调查中的每个基因的功能（即基因的转录，SNP或其他元素）的数字向量的高端基因组的位置。
strand: Object of class "numeric" a numeric vector of strand genomic position for each genomic feature under investigation: value 1 is used for "plus" (forward) strand and value -1 for "minus" (reverse) strand.
strand：Object类的"numeric"数字矢量：一个链正在调查中的每个基因组功能基因组的位置值1“加”（向前）链和价值-1用于“减” （反向）链。
chromosomesNumbers: Object of class "numeric" a numeric vector containing the list of chromosomes for which genomic annotations are provided in the GenomicAnnotations object. Each chromosome is represented just once in increasing order. Please note that chromosome usually not represented with a number must will be comverted to a number as well.
chromosomesNumbers：Object类的"numeric"数字向量的染色体基因组注释提供在GenomicAnnotations对象名单。每个染色体代表的只是一次在递增顺序。请注意，染色体通常不能代表一个数字，必须将comverted数字。
chromosomesLabels: Object of class "character" a character vector containing the list of chromosomes for which genomic annotations are provided in the GenomicAnnotations object. Each chromosome is represented just once in the same order as reported in chromosomesNumbers slot. This slot is actually used just to provide a label for each associated chromosome number, in case that some non numeric chromsome is used
chromosomesLabels：Object类的"character"字符向量的染色体基因组注释提供在GenomicAnnotations对象名单。每个染色体代表的只是一次在同一顺序报道chromosomesNumbers插槽。使用这个插槽实际上只是提供一个标签为每个相关的染色体数目的情况下，使用一些非数字染色体
optionalAnnotations: Object of class "matrix" optional annotations associated to the genomic features can be managed along with genomic positions annotations. E.g. GeneSymbol or EntrezGene ids can be associated to gene realted GenomicAnnotaitons objects. These additional annotations are not mandatory (the default value for this slot is NULL) The additional annotations must be provided as a matrix of character, with a number of rows equal to the length of "ids" slot and a number of columns equal
optionalAnnotations：类"matrix"相关基因功能的可选注释对象可以管理随着注释的基因组的位置。例如GeneSymbol或EntrezGene IDS可以关联到基因realted GenomicAnnotaitons对象。这些额外的注解是不是强制性的（此插槽的默认值是NULL），必须提供额外的注解作为一个字符矩阵的行数等于“IDS”槽的长度和列数相等，
optionalAnnotationsHeaders: Object of class "character" character vector containing the names associated to optional annotations. Please avoid using spaces in annotations names.
optionalAnnotationsHeaders类"character"字符包含可选的注释关联的名称的矢量对象。请避免使用注释名称空间。
statistic: Object of class "matrix" a numeric matrix containing gene-centered statistics (or statistics on genomic data centered on other genomic features under investigation). The statistics must be provided as a matrix of numeric values, with a number of rows equal to the length of "ids" slot and a number of columns equal
statistic：Object类的"matrix"数字矩阵，含有基因中心的统计数据（或集中在受调查的其他基因组功能基因组数据的统计资料）。必须提供的统计数据作为一个数值矩阵，与行数等于“IDS”槽的长度和列数相等
延伸----------Extends----------
Class "PREDAResults", directly. Class "DataForPREDA", directly. Class "GenomicAnnotationsForPREDA", by class "PREDAResults", distance 2. Class "StatisticsForPREDA", by class "DataForPREDA", distance 2. Class "GenomicAnnotations", by class "PREDAResults", distance 3.
类"PREDAResults"，直接。类"DataForPREDA"，直接。类"GenomicAnnotationsForPREDA"，由类“PREDAResults”，距离为2。类"StatisticsForPREDA"，类“DataForPREDA”，距离为2。类"GenomicAnnotations"，由类“PREDAResults”，距离3。
方法----------Methods----------
GenomicAnnotationsSortAndCleanNA signature(.Object = "PREDADataAndResults"): sort annotations according to selected chromosomes and to remove genes containing any NA annotation field
GenomicAnnotationsSortAndCleanNAsignature(.Object = "PREDADataAndResults")：根据选定的染色体和基因删除含有任何NA注释字段的排序注解
initialize signature(.Object = "PREDADataAndResults"): initialize method for PREDADataAndResults objects
初始化signature(.Object = "PREDADataAndResults")：PREDADataAndResults对象初始化方法
PREDADataAndResults2dataframe signature(.Object = "PREDADataAndResults"): extract data and annotations as a dataframe with probeids as rownames
PREDADataAndResults2dataframesignature(.Object = "PREDADataAndResults")：提取数据，并作为与作为rownames probeids dataframe注解
注意----------Note----------
This class is better described in the package vignette
这个类是更好地描述包中的小插曲
作者（S）----------Author(s)----------
Francesco Ferrari
参见----------See Also----------
"GenomicAnnotations", "GenomicAnnotationsForPREDA", "StatisticsForPREDA", "DataForPREDA", "PREDAResults", GenomicAnnotationsSortAndCleanNA,PREDADataAndResults2dataframe
"GenomicAnnotations"，"GenomicAnnotationsForPREDA"，"StatisticsForPREDA"，"DataForPREDA"，"PREDAResults"，GenomicAnnotationsSortAndCleanNA，PREDADataAndResults2dataframe
举例----------Examples----------
showClass("PREDADataAndResults")
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 2012-2-26 11:24:54
