R语言 REDseq包 assignSeq2REsite()函数中文帮助文档(中英文对照)

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assignSeq2REsite(REDseq)
assignSeq2REsite()所属R语言包：REDseq

                                         Assign mapped sequence tags to corresponding restriction enzyme (RE) cut sites
                                         映射序列标签分配到相应的限制性内切酶（RE）的切割网站

                                         译者：生物统计家园网 机器人LoveR

描述----------Description----------

Given the sequence tags aligned to a genome as a RangedData, and a map built using the buildREmap function, assignSeq2REsite first identifies RE sites that have mapped sequence tags around the cut position taking consideration of user-defined offset, sequence length and strand in the aligned sequences. These RE sites are used as seeds for assigning the remaining tags depending on which of five strategies the users select for partitioning sequences associated with multiple RE sites, i.e., unique, average,estimate, best and random.
鉴于序列标签对齐到作为RangedData基因，并建立使用buildREmap功能的图，assignSeq2REsite首先确定重新映射周围切割的位置，在考虑用户定义的偏移，序列的长度和钢绞线对齐序列标签的网站序列。这些的RE站点分配剩余的标记，根据五大战略，用户选择分区关联的多个稀土网站，即独特的，平均估计，最好的和随机的序列作为种子。


用法----------Usage----------


assignSeq2REsite(input.RD, REmap.RD, cut.offset = 1, seq.length = 36,
allowed.offset = 5, min.FragmentLength = 60, max.FragmentLength = 300,  
partitionMultipleRE = c("unique", "average", "estimate","best", "random"))



参数----------Arguments----------

参数：input.RD
RangedData as mapped sequences: see example below  
映射序列RangedData：见下面的例子


参数：REmap.RD
RangedData as restriction enzyme (RE) cut site map: see example below  
限制性内切酶（RE）的切割站点图RangedData：见下面的例子


参数：cut.offset
The cut offset from the start of the RE recognition sequence: index is 0 based, i.e.,1 means the RE cuts at position 2.   
切：从稀土识别序列的开始抵消指数是0基础，即，1表示在位置2再削减。


参数：seq.length
Sequence length: 36 means that the sequence tags are 36-base long.   
序列的长度：36序列标签是长36碱基的手段。


参数：allowed.offset
Offset allowed to count for imperfect sticky end repair and primer addition.  
偏移允许算不完善粘底维修和底漆此外，。


参数：min.FragmentLength
Minimum fragment length of the sequences size-selected for sequencing  
最小的序列片段长度的大小选择测序


参数：max.FragmentLength
Maximum fragment length of the sequences size-selected for sequencing  
最大序列片段长度的大小选择测序


参数：partitionMultipleRE
The strategy for partitioning sequences associated with multiple RE sites. For strategy unique, only sequence tags that are associated with a unique RE site within the distance between min.FragmentLength and max.FragmentLength are kept for downstream analysis. For strategy average, sequence tags are partitioned equally among associated RE sites. For strategy estimate, sequence tags are partitioned among associated RE sites with a weight function, which is determined using the count distribution of the RE seed sites described in the description section above. For strategy best, sequence tags are assigned to the most probable RE sties with the same weight function as that in strategy estimate. For strategy random, the sequence tags are randomly assigned to one of the multiple associated RE sites.  
战略分区与多个稀土站点相关的序列。对于战略的独特的，唯一的序列标签独特的稀土网站内之间min.FragmentLength和max.FragmentLength距离保持为下游分析。战略平均序列标签分区同样相关稀土站点之间。战略估计，序列标签，分区之间的权函数使用上面的描述节中所述的再生种子网站的数量分布，这是确定的相关稀土网站。为最好的策略，序列标签分配给最有可能重新麦粒肿与相同重量的战略估计功能。策略随机序列标签被随机分配到多个相关的稀土网站之一。


值----------Value----------


参数：passed.filter
Sequences assigned to RE(s), see the example r.unique$passed.filter
分配给重新（S）的序列，请参阅例如r.unique $ passed.filter的


参数：notpassed.filter
Sequences not assigned to any RE, see example r.unique$notpassed.filter
没有任何重新分配的序列，看到的例子r.unique $ notpassed.filter“


参数：mREwithDetail
Detailed assignment information for sequences associated with multiple RE sites. Only available when partitionMultipleRE is set to average or estimate, see r.estimate$mREwithDetail in the examples   </table>
为与多个稀土站点相关序列的详细分配信息。只适用于当partitionMultipleRE平均或估算，看到r.estimate“的例子$ mREwithDetail </ TABLE>


作者（S）----------Author(s)----------



Lihua Julie Zhu




参考文献----------References----------

2.Kessler, C. and V. Manta, Specificity of restriction endonucleases and DNA modification methyltransferases a review (Edition 3). Gene, 1990. 92(1-2): p. 1-248. <br> 3. Pingoud, A., J. Alves, and R. Geiger, Restriction enzymes. Methods Mol Biol, 1993. 16: p. 107-200. <br>

参见----------See Also----------

buildREMap, example.REDseq, example.map, example.assignedREDseq
buildREMap，example.REDseq，example.map，example.assignedREDseq


举例----------Examples----------


        library(REDseq)
        data(example.REDseq)
        data(example.map)
        r.unique = assignSeq2REsite(example.REDseq, example.map,
cut.offset = 1, seq.length = 36, allowed.offset = 5,
min.FragmentLength = 60, max.FragmentLength = 300,
partitionMultipleRE = "unique")
        r.average = assignSeq2REsite(example.REDseq, example.map, cut.offset = 1,
seq.length = 36, allowed.offset = 5, min.FragmentLength = 60,
max.FragmentLength = 300, partitionMultipleRE = "average")
        r.random = assignSeq2REsite(example.REDseq, example.map, cut.offset = 1,
seq.length = 36, allowed.offset = 5, min.FragmentLength = 60,
max.FragmentLength = 300, partitionMultipleRE = "random")
        r.best = assignSeq2REsite(example.REDseq, example.map, cut.offset = 1,
seq.length = 36, allowed.offset = 5, min.FragmentLength = 60,
max.FragmentLength = 300, partitionMultipleRE = "best")
        r.estimate = assignSeq2REsite(example.REDseq, example.map, cut.offset = 1,
seq.length = 36, allowed.offset = 5, min.FragmentLength = 60,
max.FragmentLength = 300, partitionMultipleRE = "estimate")
        r.estimate$passed.filter
        r.estimate$notpassed.filter

转载请注明:出自 生物统计家园网(http://www.biostatistic.net)。


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