GenomicAnnotationsForPREDA-class(PREDA)
GenomicAnnotationsForPREDA-class()所属R语言包：PREDA
Class "GenomicAnnotationsForPREDA" GenomicAnnotations class with additional slot specifying the reference position for PREDA analysis
普雷达分析类的“GenomicAnnotationsForPREDA”GenomicAnnotations额外的插槽类指定参考位置
译者：生物统计家园网 机器人LoveR
描述----------Description----------
This class is equivalent to the GenomicAnnotations class but includes an additional slot specifying the reference position that will be used for PREDA smoothing of data: this is included in the "position" slot. An unique reference position is required for PREDA analysis because this position is used for smoothing data along chromosomal coordinates. This reference position usaually is the start, the end, or the median posizion of each considered genomic feature, nevertheless other user defined positions could be used as well.
这个类是相等于的GenomicAnnotations类，但包括一个额外的插槽，数据平滑普雷达将使用指定的参考位置：这是包含在“位置”老虎。因为这个位置是用于数据平滑沿染色体坐标，需要一个独特的参考位置普雷达分析。此参考的位置usaually是开始，结束，或平均每个考虑的基因组功能posizion，但其他用户定义的位置，以及可以使用。
类的对象----------Objects from the Class----------
Objects can be created by calls of the form new("GenomicAnnotationsForPREDA", ids, chr, start, end, strand, chromosomesNumbers, chromosomesLabels, position, optionalAnnotations, optionalAnnotationsHeaders).
创建对象可以通过检测的形式new("GenomicAnnotationsForPREDA", ids, chr, start, end, strand, chromosomesNumbers, chromosomesLabels, position, optionalAnnotations, optionalAnnotationsHeaders)。
插槽----------Slots----------
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。
延伸----------Extends----------
Class "GenomicAnnotations", directly.
类"GenomicAnnotations"，直接。
方法----------Methods----------
genomePlot signature(.Object = "GenomicAnnotationsForPREDA"): draw a genome plot
genomePlotsignature(.Object = "GenomicAnnotationsForPREDA")：绘制基因组的图
GenomicAnnotations2dataframe signature(.Object = "GenomicAnnotationsForPREDA"): extract annotations as a dataframe with probeids as rownames
GenomicAnnotations2dataframesignature(.Object = "GenomicAnnotationsForPREDA")：作为一个与作为rownames probeids dataframe提取注释
GenomicAnnotationsFilter_neg signature(.Object = "GenomicAnnotationsForPREDA"): filter annotations to remove selected chromosomes
GenomicAnnotationsFilter_negsignature(.Object = "GenomicAnnotationsForPREDA")：过滤器注释删除选定的染色体
GenomicAnnotationsFilter_pos signature(.Object = "GenomicAnnotationsForPREDA"): filter annotations to keep selected chromosomes
GenomicAnnotationsFilter_possignature(.Object = "GenomicAnnotationsForPREDA")：过滤器的注释，以保持选定的染色体
GenomicAnnotationsForPREDA2dataframe signature(.Object = "GenomicAnnotationsForPREDA"): extract annotations as a dataframe with probeids as rownames
GenomicAnnotationsForPREDA2dataframesignature(.Object = "GenomicAnnotationsForPREDA")：作为一个与作为rownames probeids dataframe提取注释
GenomicAnnotationsForPREDA2GenomicAnnotations signature(.Object = "GenomicAnnotationsForPREDA"): extract the GenomicAnnotations object from the GenomicAnnotationsForPREDA object
GenomicAnnotationsForPREDA2GenomicAnnotationssignature(.Object = "GenomicAnnotationsForPREDA")：提取从GenomicAnnotationsForPREDA对象的GenomicAnnotations，对象
GenomicAnnotationsForPREDA2PREDAResults signature(.Object = "GenomicAnnotationsForPREDA"): add PREDA results information to genomic annotatations creating a PREDAResults object
GenomicAnnotationsForPREDA2PREDAResultssignature(.Object = "GenomicAnnotationsForPREDA")：添加普雷达结果信息创建PREDAResults对象的基因组annotatations
GenomicAnnotationsSortAndCleanNA signature(.Object = "GenomicAnnotationsForPREDA"): sort annotations according to selected chromosomes and to remove genes containing any NA annotation field
GenomicAnnotationsSortAndCleanNAsignature(.Object = "GenomicAnnotationsForPREDA")：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 = "GenomicAnnotationsForPREDA"): initialize method for GenomicAnnotationsForPREDA objects
初始化signature(.Object = "GenomicAnnotationsForPREDA")：GenomicAnnotationsForPREDA对象的初始化方法
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", GenomicAnnotationsSortAndCleanNA, GenomicAnnotationsForPREDA2PREDAResults,GenomicAnnotationsForPREDA2GenomicAnnotations, GenomicAnnotationsForPREDA2dataframe,GenomicAnnotationsFilter_pos, GenomicAnnotationsFilter_neg,GenomicAnnotations2dataframe,genomePlot
"GenomicAnnotations"，GenomicAnnotationsSortAndCleanNA，GenomicAnnotationsForPREDA2PREDAResults，GenomicAnnotationsForPREDA2GenomicAnnotations，GenomicAnnotationsForPREDA2dataframe，GenomicAnnotationsFilter_pos，GenomicAnnotationsFilter_neg，GenomicAnnotations2dataframe，genomePlot
举例----------Examples----------
showClass("GenomicAnnotationsForPREDA")
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 11:22:32
