R语言 PREDA包 GenomicAnnotations-class()函数中文帮助文档(中英文对照)

loveR

GenomicAnnotations-class(PREDA)
GenomicAnnotations-class()所属R语言包：PREDA

                                        Class "GenomicAnnotations" to manage information about genomic features
                                         类“GenomicAnnotations”管理有关的基因组功能的信息

                                         译者：生物统计家园网 机器人LoveR

描述----------Description----------

This class is used to manage information about genomic features under investigation: i.e. genomic genes, SNP or others, with particular focus on the genomic coordinates of each of them.
这个类是用来管理正在调查有关的基因组功能的信息：即基因组的基因，SNP或他人，特别注重对他们每个人的基因组坐标。


类的对象----------Objects from the Class----------

Objects can be created by calls of the form new("GenomicAnnotations", ids, chr, start, end, strand, chromosomesNumbers, chromosomesLabels, optionalAnnotations, optionalAnnotationsHeaders).
创建对象可以通过检测的形式new("GenomicAnnotations", ids, chr, start, end, strand, chromosomesNumbers, chromosomesLabels, optionalAnnotations, optionalAnnotationsHeaders)。


插槽----------Slots----------




ids: Object of class "character" ~~
ids：Object类的"character"~~




chr: Object of class "integer" ~~
chr：Object类的"integer"~~




start: Object of class "integer" ~~
start：Object类的"integer"~~




end: Object of class "integer" ~~
end：Object类的"integer"~~




strand: Object of class "numeric" ~~
strand：Object类的"numeric"~~




chromosomesNumbers: Object of class "numeric" ~~
chromosomesNumbers：Object类的"numeric"~~




chromosomesLabels: Object of class "character" ~~
chromosomesLabels：Object类的"character"~~




optionalAnnotations: Object of class "matrix" ~~
optionalAnnotations：Object类的"matrix"~~




optionalAnnotationsHeaders: Object of class "character" ~~
optionalAnnotationsHeaders：Object类的"character"~~


方法----------Methods----------




GenomicAnnotations2dataframe signature(.Object = "GenomicAnnotations"): extracts annotations as a dataframe with probeids as rownames
GenomicAnnotations2dataframesignature(.Object = "GenomicAnnotations")：提取注释作为与作为rownames probeids dataframe




GenomicAnnotations2GenomicAnnotationsForPREDA signature(.Object = "GenomicAnnotations"): generate a new GenomicAnnotationsForPREDA object from a GenomicAnnotations object
GenomicAnnotations2GenomicAnnotationsForPREDAsignature(.Object = "GenomicAnnotations")：生成从GenomicAnnotations对象的新GenomicAnnotationsForPREDA对象




GenomicAnnotations2reference_positions signature(.Object = "GenomicAnnotations"): extract from the GenomicAnnotations object a vector containing a vector with reference positions
GenomicAnnotations2reference_positionssignature(.Object = "GenomicAnnotations")：从的GenomicAnnotations提取反对一个向量，包含一个矢量与参考位置




GenomicAnnotationsExtract signature(.Object = "GenomicAnnotations"): extract optional annotations for a specific region
GenomicAnnotationsExtractsignature(.Object = "GenomicAnnotations")：为一个特定的区域中提取的可选注释




GenomicAnnotationsFilter_neg signature(.Object = "GenomicAnnotations"): filter annotations to remove selected chromosomes
GenomicAnnotationsFilter_negsignature(.Object = "GenomicAnnotations")：过滤器注释删除选定的染色体




GenomicAnnotationsFilter_pos signature(.Object = "GenomicAnnotations"): filter annotations to keep selected chromosomes
GenomicAnnotationsFilter_possignature(.Object = "GenomicAnnotations")：过滤器的注释，以保持选定的染色体




GenomicAnnotationsSortAndCleanNA signature(.Object = "GenomicAnnotations"): sort annotations according to selected chromosomes and to remove genes containing any NA annotation field
GenomicAnnotationsSortAndCleanNAsignature(.Object = "GenomicAnnotations")：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




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




initialize signature(.Object = "GenomicAnnotations"): initialize method for GenomicAnnotations objects
初始化signature(.Object = "GenomicAnnotations")：GenomicAnnotations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----------

GenomicAnnotations2dataframe, GenomicAnnotations2GenomicAnnotationsForPREDA,  GenomicAnnotations2reference_positions,GenomicAnnotationsExtract, GenomicAnnotationsFilter_neg,GenomicAnnotationsFilter_pos, GenomicAnnotationsSortAndCleanNA,GenomicRegionsAnnotate,
GenomicAnnotations2dataframe，GenomicAnnotations2GenomicAnnotationsForPREDA，GenomicAnnotations2reference_positions，GenomicAnnotationsExtract，GenomicAnnotationsFilter_neg，GenomicAnnotationsFilter_pos，GenomicAnnotationsSortAndCleanNA，GenomicRegionsAnnotate


举例----------Examples----------


showClass("GenomicAnnotations")

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。