mergeBreakpoints(R453Plus1Toolbox)
mergeBreakpoints()所属R语言包：R453Plus1Toolbox
Identify and merge related breakpoints caused by the same variant.
识别和合并相同的变种所造成的相关断点。
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Structural variation like transversions or inversion cause two breakpoints. In the context of fusion genes, these are called the pathogenic breakpoint and the reciproce breakpoint. The method detectBreakpoints processes each breakpoint individually and does explicitly not put reads from the pathogenic and reciproce breakpoint into the same cluster. Hence, it is usually sensible to call this methods afterward to search for related pairs of breakpoints to gain more confidence about the existence of a structural variation.
像颠或反转结构的变化导致了两个断点。在融合基因的情况下，这些被称为病原断点和reciproce断点的。 的方法detectBreakpoints处理每个断点单独和并没有明确地把读取到同一聚类中的致病性和reciproce断点。因此，它通常是明智的调用这个方法之后，搜索相关双断点存在结构性变化，以获取更多的信心。
用法----------Usage----------
mergeBreakpoints(breakpoints, maxDist, mergeBPs)
参数----------Arguments----------
参数：breakpoints
An object of class Breakpoints storing the breakpoints that will (potentially) be merged.
一个类的对象Breakpoints存储，将（可能）被合并的断点。
参数：maxDist
The maximal distance in basepairs at which two breakpoints will be merged. Default value is 1000.
在碱基对在这两个断点将被合并的最大距离。默认值是1000。
参数：mergeBPs
An optional list of vectors of length two giving the breakpoints that should be merged. If this argument is given, the method will not search for related breakpoints.
可选列表的长度为2的向量，提供的，应当合并断点。如果此参数，该方法不会搜寻相关的断点。
Details
详情----------Details----------
If the maxDist argument is given, the method compares each pair of breakpoints and checks, whether the two breakpoints may belong to the same structural variation. In addition to the spanned chromosomes, the orientation and the strand information of the reads spanning the breakpoints are also compared for this purpose. If chrosmosome, orientation and strand information of two breakpoints go well together, they will be merged, if the absolute distance of the breakpoints on chromosome A plus the absolute distance on chromosome B is smaller or equal to maxDist. If one breakpoint has more than one potential mate breakpoint for merging, it will be merged with the first candidate and a warning message is printed. The default value of maxDist is 1000.\
如果maxDist参数，该方法比较对每个断点和检查，两个断点是否可能属于相同的结构变化。除了跨区染色体，方向和钢绞线信息读取跨越断点，也为这一目的相比。如果chrosmosome，方向和钢绞线的两个断点的信息一起去的，他们将被合并，如果断点号染色体上的绝对距离一个加号染色体上的乙的绝对距离是小于或等于maxDist。如果一个断点合并有多个潜在的队友断点，将被合并的第一候选人，并打印一条警告消息。 maxDist默认值是1000。\
If the mergeBPs argument is given, the method will not search for related breakpoints but simply merge the given breakpoints. mergeBPs must be a list with vectors of length two that either contain the names of the indices of the breakpoints that should be merged.\
如果给出mergeBPs参数，该方法将不搜索相关断点，但简单的合并给定的断点。 mergeBPs必须是一个长度为二的向量，包含断点指数的名称应合并list与\
The arguments maxDist and mergeBPs cannot be given together. The given Breakpoints object must not contain breakpoints that have been merged before.
论据maxDist和mergeBPs不能得到一起。给定的Breakpoints对象必须不包含已合并前的断点。
值----------Value----------
An object of class Breakpoints storing merged and unmerged breakpoints.
一个对象类Breakpoints存储合并和未合并断点。
作者（S）----------Author(s)----------
Hans-Ulrich Klein
参见----------See Also----------
detectBreakpoints, Breakpoints-class, plotChimericReads
detectBreakpoints，Breakpoints-class，plotChimericReads
举例----------Examples----------
# Load bam file and filter chimeric reads[加载BAM文件和过滤嵌合读取]
library(Rsamtools)
bamFile = system.file("extdata", "StructuralVariantDetection", "bam", "N01.bam", package="R453Plus1Toolbox")
bam = scanBam(bamFile)
data(captureArray)
linker = sequenceCaptureLinkers("gSel3")[[1]]
filterReads = filterChimericReads(bam, targetRegion=captureArray, linkerSeq=linker)
# detect breakpoints of size >= 3[检测大小断点> = 3]
breakpoints = detectBreakpoints(filterReads, minClusterSize=3)
table(breakpoints)
summary(breakpoints)
# merge breakpoints[合并断点]
breakpoints = mergeBreakpoints(breakpoints)
summary(breakpoints)
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 11:51:04
