removeLinker(R453Plus1Toolbox)
removeLinker()所属R语言包：R453Plus1Toolbox
Remove linker sequences located at the start of short reads
删除位于短读取开始的链接序列
译者：生物统计家园网 机器人LoveR
描述----------Description----------
If linkers are attached during sample preparation, it may be useful to remove the linkers' sequences after sequencing. This method finds and removes linker sequences that are located at the start of the given reads.
如果连接器附着在样品制备，它可能是有用的，取出后连接器的序列测序。这种方法查找并删除链接给读开始在位于序列。
用法----------Usage----------
## S4 method for signature 'XStringSet,DNAString,logical,numeric,numeric'
removeLinker(reads, linker, removeReadsWithoutLinker, minOverlap, penalty)
参数----------Arguments----------
参数：reads
A DNAStringSet instance that contains reads possibly having linkers at their start site
一个DNAStringSet实例，其中包含读取的起始站点可能有连接器
参数：linker
A DNAString instance with the linker's sequence
一个DNAString实例与连接器的序列
参数：removeReadsWithoutLinker
Whether reads without linkers should be removed. Default is FALSE
是否应删除没有连接器读取。默认为false
参数：minOverlap
The minimal score that must be achived when aligning the linker. Default is length(linker)/2
对准必须achived的链接的最低得分。默认情况下是长度（连接器）/ 2
参数：penalty
The penalty for substitutions or indels. Default is -2
换人或INDELS罚款。默认值是-2
Details
详情----------Details----------
The best alignment of the linker within the start (length of linker + 5) of each given sequence is computed. The followong scoring schema is used: Each matching bases scores +1. Each substitution or indel scores the given penalty argument (default: penalty=-2). There are no penalties for gaps and the end of the linker (overlap). An alignment is considered as match, if the scores is larger of equal to minOverlap (default: minOverlap=round(length(linker)/2)). In cases of a successful match, the subsequence from position 1 until the end of the linker's alignment is removed.
最好的连接器内的每一个给定序列的开始对齐（连接器的长度+ 5）计算。 followong得分模式：每个匹配碱基的分数+1。每个替代或INDEL成绩给予罚款参数（默认是：罚款= -2）。有没有差距和链接（重叠）的处罚。对齐被视为比赛中，如果分数是平等的minOverlap（默认：minOverlap =轮（长（连接器）/ 2））。在一个成功的匹配情况下，从1月底，直到连接器的对齐位置的序列被删除。
值----------Value----------
removeLinker returns a DNAStringSet with trimmed reads.
removeLinker返回一个修整读取DNAStringSet。
作者（S）----------Author(s)----------
Hans-Ulrich Klein
参见----------See Also----------
sequenceCaptureLinkers, DNAStringSet, pairwiseAlignment
sequenceCaptureLinkers，DNAStringSet，pairwiseAlignment
举例----------Examples----------
linker = sequenceCaptureLinkers()[[1]]
reads = DNAStringSet(c(
"CTCGAGAATTCTGGATCCTCAAA",
"GAATTCTGGATCCTCAAA",
"CTCGAGAAAAAAAAATCCTCAAA"))
removeLinker(reads, linker)
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 11:52:23
