filterChimericReads(R453Plus1Toolbox)
filterChimericReads()所属R语言包：R453Plus1Toolbox
Extract chimeric reads and apply filtering steps to remove artificial
提取嵌合读取和应用过滤的步骤，以消除人工
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Chimeric reads may be caused by sequencing a chromosomal aberration or by technical issues during sample preparation. This method implements several filter steps to remove false chimeric
嵌合体的读取可能导致测序的染色体畸变，或样品制备过程中的技术问题。这种方法实现了几个过滤器的步骤来消除虚假嵌合
用法----------Usage----------
## S4 method for signature 'list,RangesList,DNAString,numeric,numeric'
filterChimericReads(alnReads, targetRegion, linkerSeq, minDist, dupReadDist)
参数----------Arguments----------
参数：alnReads
A list storing the aligned reads as produced by the function scanBam.
列表存储对齐读取功能scanBam的的。
参数：targetRegion
A object of class rangesList containing the target region of e.g. a used capture array. The parameter may be omitted in case of a non targeted sequencing approach.
对象，其中包含一类rangesList的目标区域，如用于捕捉阵列。在非针对性的测序方法的情况下，该参数可以省略。
参数：linkerSeq
A linker sequence that was used during sample preparation. It may be omitted.
样品制备过程中使用一个连接器的序列。它可以被省略。
参数：minDist
The minimum distance between two local alignments (see details), default 1000
两个地方的路线之间的最短距离（见详情），默认1000
参数：dupReadDist
The maximum distance between the 5 prime start position of two duplicated reads (see details), default 1.
两个重复读取（见详情），默认为1 5黄金起始位置之间的最大距离。
Details
详情----------Details----------
The following filter steps are performed:
下面的过滤器的步骤进行：
1. All chimeric reads with exactly two local alignments are extracted. Reads with more than two local alignments are discarded.
1。所有嵌合读取两个地方的路线提取。读取与两个以上的地方路线被丢弃。
2. If the targetRegion argument is given, chimeric reads must have one local alignment at least overlapping the the target region. If both local alignments are outside the target region, the read is discarded.
2。嵌合读给出，如果targetRegion参数，必须有至少一个本地对齐重叠的目标区域。如果这两个地方的路线外的目标区域，读取被丢弃。
3. If the linkerSeq argument is given, all chimeric reads that have the linker sequence between their local alignments are removed. When searching the linker sequence, 4 mismatches or indels are allowed and the linker sequence must not start or end within the first or last ten bases of the read. The function searches for the linkerSeq and for it's reverse complement.
3。 ，如果linkerSeq参数，所有嵌合读有序列的局部比对之间的连接器将被删除。当搜索连接器的序列，允许4不匹配或INDELS和链接顺序不能启动或结束内的第一个或最后一个读十碱基。为linkerSeq和它的逆补功能搜索。
4. Two local alignment of a read must have minDist reads between the alignments (if both alignment are on the same chromosome). Otherwise, the read seems to span a deletion and not a chromosomal aberration and is discarded.
4。一读的地方对齐必须有minDist之间的路线（如果两个相同的染色体排列）读取。否则，读，似乎跨越了删除，而不是一个染色体畸变和被丢弃。
5. Duplicated reads are removed. Two reads are duplicated, if the lie on the same strand and have the same 5 prime start position. Due to sequencing and alignment errors, the start position may vary for a maximum of dupReadDist bases. In case of duplicated reads, only the longest read is kept.
5。重复读取被删除。两次读取是重复的，如果在同一链的谎言，并有相同的5个首要的开始位置。由于测序和对齐错误，起始位置可能会有所不同最大的dupReadDist碱基。在重复读取，只有保持最长的读取情况。
Reads passing all filtering steps are returned in the list structure as given by the alnReads argument (as derived from the scanBam method). A data frame with information about the number of reads that passed each filter is added to the list.
所有过滤步骤list结构alnReads参数（从scanBam方法而得）返回读通过。一个数据框，通过每个过滤器读取信息被添加到列表。
值----------Value----------
A list containing only filtered chimeric reads. The list has the same structure like the given argument alnReads. Additionally, one element “log” with logging
一个list只包含过滤嵌合读。 list具有相同的结构像给定的参数alnReads。此外，一个元素与记录“登录”
作者（S）----------Author(s)----------
Hans-Ulrich Klein
参见----------See Also----------
detectBreakpoints, mergeBreakpoints, Breakpoints-class,
detectBreakpoints，mergeBreakpoints，Breakpoints-class
举例----------Examples----------
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)
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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 11:49:41
