R语言 R453Plus1Toolbox包 Breakpoints-class()函数中文帮助文档(中英文对照)

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Breakpoints-class(R453Plus1Toolbox)
Breakpoints-class()所属R语言包：R453Plus1Toolbox

                                        Class "Breakpoints"
                                         班“断点”

                                         译者：生物统计家园网 机器人LoveR

描述----------Description----------

Container to store chimeric reads that were clustered to putative breakpoints indicating structural variants. Related information like breakpoint position or alignment information about the chimeric reads is stored as well.
集装箱存储嵌合读取聚表明结构变异的假定断点。断点位置或对齐有关嵌合读取的信息等相关信息以及存储。


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

Objects can be created by calls of the form new("Breakpoints", ...). Usually, objects will be created by calling the detectBreakpoints method. It is not intended that users create objects of this class manually.
创建对象可以通过检测的形式new("Breakpoints", ...)。通常，对象将被创建调用detectBreakpoints方法。它的目的不是用户手动创建这个类的对象。

All slots of this class can be found twice. One slot name ends with “C1” and the other “C2”. The slots labeled with “C2” are empty until mergeBreakpoints has been called and contain information about putativly associated breakpoints detected by mergeBreakpoints.
这个类的所有插槽都可以找到两次。一个插槽名称“C1”和其他的“C2”结束。 “C2”标记的插槽是空的，直到mergeBreakpoints已被称为包含putativly相关的检测由mergeBreakpoints断点信息。


插槽----------Slots----------




seqsC1: Object of class "list" with one data frame for each breakpoint. The data frame stores all chimeric reads covering the first breakpoint together with the alignment
seqsC1：Object类的"list"一个数据框每个断点。数据框的存储读取所有嵌合覆盖第一个断点，连同对齐




seqsC2: Object of class "list" with one data frame for each breakpoint. The data frame stores all chimeric reads covering the second breakpoint together with the alignment
seqsC2：Object类的"list"一个数据框每个断点。连同对齐数据框存储读取所有嵌合覆盖第二个断点




commonBpsC1: Object of class "list" with one data frame for each breakpoint. The data frame stores the consensus breakpoint sequence as well as the breakpoint
commonBpsC1：Object类的"list"一个数据框每个断点。数据框存储的共识断点序列以及断点




commonBpsC2: Object of class "list" with one data frame for each breakpoint. The data frame stores the consensus breakpoint sequence as well as the breakpoint
commonBpsC2：Object类的"list"一个数据框每个断点。数据框存储的共识断点序列以及断点




commonAlignC1: Object of class "list" with one object of class PairwiseAlignedFixedSubject-class for each breakpoint storing the alignments of the chimeric reads against the consensus breakpoint sequence for the
commonAlignC1：Object类的"list"一类的对象PairwiseAlignedFixedSubject-class每个存储嵌合路线的断点对共识断点序列读取的




commonAlignC2: Object of class "list" with one object of class PairwiseAlignedFixedSubject-class for each breakpoint storing the alignments of the chimeric reads against the consensus breakpoint sequence for the
commonAlignC2：Object类的"list"一类的对象PairwiseAlignedFixedSubject-class每个存储嵌合路线的断点对共识断点序列读取的




alignedReadsC1: Object of class "list" with one object of class AlignedRead-class storing all
alignedReadsC1：Object类的"list"一类的对象AlignedRead-class储存所有




alignedReadsC2: Object of class "list" with one object of class AlignedRead-class storing all
alignedReadsC2：Object类的"list"一类的对象AlignedRead-class储存所有


方法----------Methods----------




alignedReadsC1<- signature(object = "Breakpoints",         value = "list"):
alignedReadsC1 < - signature(object = "Breakpoints",         value = "list")：




alignedReadsC1 signature(object = "Breakpoints"):
alignedReadsC1signature(object = "Breakpoints")：




alignedReadsC2<- signature(object = "Breakpoints",         value = "list"):
alignedReadsC2 < - signature(object = "Breakpoints",         value = "list")：




alignedReadsC2 signature(object = "Breakpoints"):
alignedReadsC2signature(object = "Breakpoints")：




commonAlignC1<- signature(object = "Breakpoints",         value =  "list"):
commonAlignC1 < - signature(object = "Breakpoints",         value =  "list")：




commonAlignC1 signature(object = "Breakpoints"):
commonAlignC1signature(object = "Breakpoints")：




commonAlignC2<- signature(object = "Breakpoints",         value = "list"):
commonAlignC2 < - signature(object = "Breakpoints",         value = "list")：




commonAlignC2 signature(object = "Breakpoints"):
commonAlignC2signature(object = "Breakpoints")：




commonBpsC1<- signature(object = "Breakpoints",         value = "list"):
commonBpsC1 < - signature(object = "Breakpoints",         value = "list")：




commonBpsC1 signature(object = "Breakpoints"):
commonBpsC1signature(object = "Breakpoints")：




commonBpsC2<- signature(object = "Breakpoints",         value = "list"):
commonBpsC2 < - signature(object = "Breakpoints",         value = "list")：




commonBpsC2 signature(object = "Breakpoints"):
commonBpsC2signature(object = "Breakpoints")：




seqsC1<- signature(object = "Breakpoints",         value =        "list"):
seqsC1 < - signature(object = "Breakpoints",         value =        "list")：




seqsC1 signature(object = "Breakpoints"):
seqsC1signature(object = "Breakpoints")：




sqsC2<- signature(object = "Breakpoints",         value = "list"):
sqsC2 < - signature(object = "Breakpoints",         value = "list")：




seqsC2 signature(object = "Breakpoints"):
seqsC2signature(object = "Breakpoints")：




[ signature(x = "Breakpoints", i = "ANY", j = "ANY"):
[signature(x = "Breakpoints", i = "ANY", j = "ANY")：




length signature(x = "Breakpoints"):
长度signature(x = "Breakpoints")：




mergeBreakpoints signature(breakpoints = "Breakpoints",         maxDist = "missing", mergeBPs = "list"):
mergeBreakpointssignature(breakpoints = "Breakpoints",         maxDist = "missing", mergeBPs = "list")：




mergeBreakpoints signature(breakpoints = "Breakpoints",         maxDist = "missing", mergeBPs = "missing"):
mergeBreakpointssignature(breakpoints = "Breakpoints",         maxDist = "missing", mergeBPs = "missing")：




mergeBreakpoints signature(breakpoints = "Breakpoints",         maxDist = "numeric", mergeBPs = "missing"):
mergeBreakpointssignature(breakpoints = "Breakpoints",         maxDist = "numeric", mergeBPs = "missing")：




names<- signature(x = "Breakpoints", value = "ANY"):
名称< - signature(x = "Breakpoints", value = "ANY")：




names signature(x = "Breakpoints"):
名称signature(x = "Breakpoints")：




plotChimericReads signature(brpData = "Breakpoints"): Plot the structural variant and the chimeric reads covering its
plotChimericReadssignature(brpData = "Breakpoints")：图结构变异和嵌合内容涵盖其




summary signature(object = "Breakpoints"):
摘要signature(object = "Breakpoints")：




table signature(... = "Breakpoints"):
表signature(... = "Breakpoints")：


作者（S）----------Author(s)----------



Hans-Ulrich Klein, Christoph Bartenhagen




参见----------See Also----------

filterChimericReads, detectBreakpoints, mergeBreakpoints, plotChimericReads
filterChimericReads，detectBreakpoints，mergeBreakpoints，plotChimericReads

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