R语言 seqinr包 extract.breakpoints()函数中文帮助文档(中英文对照)

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extract.breakpoints(seqinr)
extract.breakpoints()所属R语言包：seqinr

                                        Extraction of breakpoint positions on the
                                         提取的断点位置上

                                         译者：生物统计家园网 机器人LoveR

描述----------Description----------

Extraction of breakpoint positions on the rearranged nucleotide skews.
提取的断点位置的重新排列核苷酸倾斜。


用法----------Usage----------


extract.breakpoints(rearr.ori,type = c("atfw", "atrev", "gcfw", "gcrev"), nbreaks, gridsize = 100, it.max = 500)



参数----------Arguments----------

参数：rearr.ori
A data frame obtained with the rearranged.oriloc function.   
一个数据框获得rearranged.oriloc功能。


参数：type
The type of skew for which to extract the breakpoints; must be a subset of c("atfw","atrev","gcfw","gcrev").
提取的断点，歪斜的类型必须是一个子集c("atfw","atrev","gcfw","gcrev")。


参数：nbreaks
The number of breakpoints to extract for each type of skew. Provide a vector of the same length as type.
断点的数目，以提取用于每种类型的歪斜。提供一种向量的相同的长度type。


参数：gridsize
To make sure that the best breakpoints are found, and to avoid finding only a local extremum of the likelihood and residual sum of square functions, a grid search is performed. The search for breakpoints is repeated gridsize times, with different starting values for the breakpoints.  
为了确保最好的断点被发现，一个网格，并避免只发现局部极值的可能性和残差的平方函数进行搜索。断点的搜索重复gridsize次，用不同的初始值的断点。


参数：it.max
The maximum number of iterations to be performed when searching for the breakpoints. This argument corresponds to the it.max argument in segmented.
最大迭代次数的断点时要执行的搜索。这个参数对应的it.max在segmented参数。


Details

详细信息----------Details----------

This method uses the segmented function in the segmented package to extract the breakpoints positions in the rearranged nucleotide skews obtained with the rearranged.oriloc function. To make sure that the best breakpoints are found, and to avoid finding only a local extremum of the likelihood and residual sum of square functions, a grid search is performed. The search for breakpoints is repeated gridsize times, with different starting values for the breakpoints.
此方法使用segmented功能，segmented包中提取的断点位置在重新排列的核苷酸倾斜rearranged.oriloc功能的。为了确保最好的断点被发现，一个网格，并避免只发现局部极值的可能性和残差的平方函数进行搜索。断点的搜索重复gridsize次，用不同的初始值的断点。


值----------Value----------

This function returns a list, with as many elements as the type argument (for example $gcfw will contain the results for the rearranged GC-skew, for forward-encoded genes). Each element of this list is also a list, containing the following information: in  $breaks the position of the breakpoints on the rearranged chromosome; in  $slopes.left the slopes of the segments on the left side of each breakpoint; in  $slopes.right the slopes of the segments on the right side of each breakpoint; in $real.coord, the coordinates of the breakpoints on the real chromosome (before rearrangement).
此函数返回一个列表，与type参数（例如$gcfw将包含重新排列的GC-歪斜的结果，前瞻性编码的基因）一样多的元素。这个列表的每个元素也是一个列表，包含以下信息：$breaks的位置重新排列的染色体上的断点; $slopes.left每个断点左侧的山坡上段; $slopes.right的斜坡段在右侧的每个断点;在$real.coord，真正的染色体上的断点（前重排）的坐标。


（作者）----------Author(s)----------


A. Necsulea



参考文献----------References----------


the effect of replication on DNA base composition asymmetry.

参见----------See Also----------

oriloc, draw.rearranged.oriloc,
oriloc，draw.rearranged.oriloc，


实例----------Examples----------



### Example for Chlamydia trachomatis ####[沙眼衣原体＃＃＃＃＃＃示例]

### Rearrange the chromosome and compute the nucleotide skews ###[＃＃＃＃＃＃重新排列的染色体，并计算核苷酸倾斜]

## Not run: r.ori &lt;- rearranged.oriloc(seq.fasta = system.file("sequences/ct.fasta",package = "seqinr"),[＃运行：r.ori < -  rearranged.oriloc（seq.fasta。系统（序列/ ct.fasta“，”包=“seqinr）]
    g2.coord = system.file("sequences/ct.coord",package = "seqinr"))
## End(Not run)[＃（不执行）]

### Extract the breakpoints for the rearranged nucleotide skews ###[＃＃提取断点重新排列的核苷酸倾斜＃＃＃]


## Not run: breaks &lt;- extract.breakpoints(r.ori,type = c("gcfw", "gcrev"), nbreaks = c(2, 2), gridsize = 50, it.max = 100)[＃不运行：截断 -  extract.breakpoints（r.ori，类型= C（“GCFW”，“gcrev”），nbreaks，= C（2,2），gridsize = 50，it.max = 100）]


### Draw the rearranged nucleotide skews and place the position of the breakpoints on the graphics ###[＃＃绘制的重排核苷酸的歪曲和放置断点的位置上的图形＃＃＃]

## Not run: draw.rearranged.oriloc(r.ori, breaks.gcfw = breaks$gcfw$breaks, breaks.gcrev = breaks$gcrev$breaks)[＃不运行：draw.rearranged.oriloc（r.ori中，breaks.gcfw突破$ GCFW $截断，breaks.gcrev =的突破gcrev $ $时间）]

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


注：
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