GenomicRegions-class(PREDA)
GenomicRegions-class()所属R语言包：PREDA
Class "GenomicRegions" is used to manage information about genomic regions
用于类“GenomicRegions”管理有关的基因组区域的信息
译者：生物统计家园网 机器人LoveR
描述----------Description----------
This class is used to manage genomic regions information that can be derived from PREDA analysis results
这个类是用来管理普雷达分析结果，可以从派生的基因组区域信息
类的对象----------Objects from the Class----------
Objects can be created by calls of the form new("GenomicRegions", chr, start, end, chromosomesNumbers, chromosomesLabels, optionalAnnotations, optionalAnnotationsHeaders, ids).
创建对象可以通过检测的形式new("GenomicRegions", chr, start, end, chromosomesNumbers, chromosomesLabels, optionalAnnotations, optionalAnnotationsHeaders, ids)。
插槽----------Slots----------
chr: Object of class "integer" a numeric vector representing the chromosome where each genomic region is located. Please note that chromosome usually not represented with a number must will be comverted to a number as well. e.g. for Human, chromsomomes X and Y will be converted to chromsomes 23 and 24 respectively.
chr：Object类的"integer"一个数字代表每个基因组区域位于染色体的向量。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，chromsomomes 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 region. This vector must have the same length of "chr" slot.
start：Object类的"integer"一开始每个基因组区域的基因组位置的数字向量。这种向量必须具有相同长度的“CHR”老虎。
end: Object of class "integer" a numeric vector of end genomic position for each genomic region. This vector must have the same length of "chr" slot.
end：Object类的"integer"一年底，每个基因组区域的基因组位置的数字向量。这种向量必须具有相同长度的“CHR”老虎。
chromosomesNumbers: Object of class "numeric" a numeric vector containing the list of chromosomes associated to genomic regions in the GenomicRegions object. Each chromosome is represented just once in increasing order. Please note that chromosomes usually not represented with a number will be comverted to a number as well.
chromosomesNumbers：Object类的"numeric"数字向量的染色体相关的基因组区域在GenomicRegions对象名单。每个染色体代表的只是一次在递增顺序。请注意，通常不以数字代表染色体将comverted数字。
chromosomesLabels: Object of class "character" a character vector containing the list of chromosomes associated to genomic regions in the GenomicRegions 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"字符向量的染色体相关的基因组区域在GenomicRegions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 regions can be managed along with GenomicRegions objects. E.g. the list of GeneSymbol or EntrezGene ids associated to each genomic region can be provided as optional annotation. 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 "chr", "start" and "end" slots and a number of columns equal
optionalAnnotations：类"matrix"相关的基因组区域可选注释对象可以管理随着GenomicRegions对象。例如相关GeneSymbol每个基因组区域或EntrezGene IDS名单可以提供可选的注释。这些额外的注解是不是强制性的（此插槽的默认值是NULL）的额外注解，必须提供一个字符矩阵，用“CHR”的长度等于行数，“开始”和“结束“插槽和一个数列等于
optionalAnnotationsHeaders: Object of class "character" the list of names associated to optional annotations. Please avoid using spaces in annotations names.
optionalAnnotationsHeaders类"character"可选注释关联的名称列表中的对象。请避免使用注释名称空间。
ids: Object of class "character" a character vector of unique identifiers associated to each genomic regions. This is just an optional element of GenomicRegions objects: the default value is NULL.
ids：Object类的"character"每个基因组区域相关联的唯一标识符的字符向量。这仅仅是一个可选的元素GenomicRegions对象：默认值是NULL。
方法----------Methods----------
GenomicRegions2dataframe signature(.Object = "GenomicRegions"): extract genomic regions information as a dataframe object
GenomicRegions2dataframesignature(.Object = "GenomicRegions")：提取的基因组区域信息作为dataframe对象
GenomicRegionsAnnotate signature(.Object1 = "GenomicRegions", .Object2 = "GenomicAnnotations"): extract annotations from a GenomicAnnotations object for a set of regions specified as a GenomicRegions object
GenomicRegionsAnnotatesignature(.Object1 = "GenomicRegions", .Object2 = "GenomicAnnotations")提取注解：从一组指定区域作为GenomicRegions对象GenomicAnnotations对象
GenomicRegionsChrNumber signature(.Object = "GenomicRegions"): determine the number of chromosomes with genomic regions
GenomicRegionsChrNumbersignature(.Object = "GenomicRegions")：确定染色体与基因组区域
GenomicRegionsComparison signature(.Object1 = "GenomicRegions", .Object2 = "GenomicRegions"): compare GenomicRegions objects to identify overlaps
GenomicRegionsComparisonsignature(.Object1 = "GenomicRegions", .Object2 = "GenomicRegions")：比较GenomicRegions对象，以确定重叠
GenomicRegionsCreateRegionsIds signature(.Object = "GenomicRegions"): generate unique ids for GenomicRegions objects
GenomicRegionsCreateRegionsIdssignature(.Object = "GenomicRegions")：GenomicRegions对象生成唯一的ID
GenomicRegionsFilter_neg signature(.Object = "GenomicRegions"): filter genomic regions to remove selected chromosomes
GenomicRegionsFilter_negsignature(.Object = "GenomicRegions")：过滤器的基因组区域，以删除选定的染色体
GenomicRegionsFilter_pos signature(.Object = "GenomicRegions"): filter genomic regions to keep selected chromosomes
GenomicRegionsFilter_possignature(.Object = "GenomicRegions")：过滤器的基因组区域，以保持选定的染色体
GenomicRegionsNumber signature(.Object = "GenomicRegions"): determine the number of genomic regions
GenomicRegionsNumbersignature(.Object = "GenomicRegions")：确定的基因组区域
GenomicRegionsSpan signature(.Object = "GenomicRegions"): determine the span of each genomic region
GenomicRegionsSpansignature(.Object = "GenomicRegions")：确定每个基因组区域的跨度
GenomicRegionsTotalSpan signature(.Object = "GenomicRegions"): determine the total span of genomic regions
GenomicRegionsTotalSpansignature(.Object = "GenomicRegions")：确定的基因组区域的总跨度
initialize signature(.Object = "GenomicRegions"): initialize method for GenomicRegions objects
初始化signature(.Object = "GenomicRegions")：GenomicRegions对象初始化方法
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----------
GenomicAnnotationsSortAndCleanNA,PREDADataAndResults2dataframe
GenomicAnnotationsSortAndCleanNA，PREDADataAndResults2dataframe
举例----------Examples----------
showClass("GenomicRegions")
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 11:23:23
