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

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findPalindromes(Biostrings)
findPalindromes()所属R语言包：Biostrings

                                        Searching a sequence for palindromes or complemented palindromes
                                         搜索回文或补充回文序列

                                         译者：生物统计家园网 机器人LoveR

描述----------Description----------

The findPalindromes and findComplementedPalindromes functions can be used to find palindromic or complemented palindromic regions in a sequence.
findPalindromes和findComplementedPalindromes功能可以用来寻找回文序列或补充回文区域。

palindromeArmLength, palindromeLeftArm, palindromeRightArm, complementedPalindromeArmLength, complementedPalindromeLeftArm and complementedPalindromeRightArm are utility functions for operating on palindromic or complemented palindromic sequences.
palindromeArmLength，palindromeLeftArm，palindromeRightArm，complementedPalindromeArmLength，complementedPalindromeLeftArm和complementedPalindromeRightArm回文或补充的回文序列操作的实用功能。


用法----------Usage----------


findPalindromes(subject, min.armlength=4, max.looplength=1, min.looplength=0, max.mismatch=0)
palindromeArmLength(x, max.mismatch=0, ...)
palindromeLeftArm(x, max.mismatch=0, ...)
palindromeRightArm(x, max.mismatch=0, ...)

findComplementedPalindromes(subject, min.armlength=4, max.looplength=1, min.looplength=0, max.mismatch=0)
complementedPalindromeArmLength(x, max.mismatch=0, ...)
complementedPalindromeLeftArm(x, max.mismatch=0, ...)
complementedPalindromeRightArm(x, max.mismatch=0, ...)



参数----------Arguments----------

参数：subject
An XString object containing the subject string, or an XStringViews object.  
一个XString对象，其中包含的主题串，或XStringViews对象。


参数：min.armlength
An integer giving the minimum length of the arms of the palindromes (or complemented palindromes) to search for.  
一个整数，回文（或补充回文）武器的最小长度，以搜寻。


参数：max.looplength
An integer giving the maximum length of "the loop" (i.e the sequence separating the 2 arms) of the palindromes (or complemented palindromes) to search for. Note that by default (max.looplength=1), findPalindromes will search for strict palindromes (or complemented palindromes) only.  
“循环”（即序列分离的2武器）的回文（或补充回文）搜索的最大长度的整数。注意，默认情况下（max.looplength=1）findPalindromes将严格的回文（或补充回文搜索）。


参数：min.looplength
An integer giving the minimum length of "the loop" of the palindromes (or complemented palindromes) to search for.  
一个整数，最小长度的“循环”的回文（或补充回文）搜索。


参数：max.mismatch
The maximum number of mismatching letters allowed between the 2 arms of the palindromes (or complemented palindromes) to search for.  
回文2武器（或补充回文）之间允许搜索不匹配字母的最大数目。


参数：x
An XString object containing a 2-arm palindrome or complemented palindrome, or an XStringViews object containing a set of 2-arm palindromes or complemented palindromes.  
一个XString对象，其中包含2组回文或补充回文，或XStringViews对象，它包含了一套2臂回文或补充回文。


参数：...
Additional arguments to be passed to or from methods.  
额外的参数被传递到或从方法。


Details

详情----------Details----------

The findPalindromes function finds palindromic substrings in a subject string. The palindromes that can be searched for are either strict palindromes or 2-arm palindromes (the former being a particular case of the latter) i.e. palindromes where the 2 arms are separated by an arbitrary sequence called "the loop".
findPalindromes函数找到一个主题串回文子串。可以搜索的回文是不是严格的回文或2臂回文（前者是后者的一个特定的情况下），即2武器被称为“循环”的任意序列分隔的回文。

Use the findComplementedPalindromes function to find complemented palindromic substrings in a DNAString subject (in a complemented palindrome the 2 arms are reverse-complementary sequences).
使用findComplementedPalindromes功能找到在DNAString主题的补充回文子串（2武器是在补充回文反向互补序列）。


值----------Value----------

findPalindromes and findComplementedPalindromes return an XStringViews object containing all palindromes (or complemented palindromes) found in subject (one view per palindromic substring found).
findPalindromes和findComplementedPalindromes返回一个XStringViews反对包含所有回文（或补充回文）subject（每回文发现子串）。

palindromeArmLength and complementedPalindromeArmLength return the arm length (integer) of the 2-arm palindrome (or complemented palindrome) x. It will raise an error if x has no arms. Note that any sequence could be considered a 2-arm palindrome if we were OK with arms of length 0 but we are not: x must have arms of length greater or equal to 1 in order to be considered a 2-arm palindrome. The same apply to 2-arm complemented palindromes. When applied to an XStringViews object x, palindromeArmLength and complementedPalindromeArmLength behave in a vectorized fashion by returning an integer vector of the same length as x.
palindromeArmLength和complementedPalindromeArmLength返回臂长（整数）2臂回文（或补充回文）x。如果x有没有武器，这将引发一个错误。请注意，任何序列可以被认为是2型臂回文如果我们确定长度为0的武器，但我们是不是：x必须有武器的长度大于或等于1，以被视为2臂回文。同样适用于2臂补充回文。当应用到XStringViews对象x，palindromeArmLength和complementedPalindromeArmLength在矢量时尚行为为x返回相同长度的整数向量。

palindromeLeftArm and complementedPalindromeLeftArm return an object of the same class as the original object x and containing the left arm of x.
palindromeLeftArm和complementedPalindromeLeftArm返回原始对象x包含x左臂同一类的对象。

palindromeRightArm does the same as palindromeLeftArm but on the right arm of x.
palindromeRightArm不为palindromeLeftArm但x右臂相同。

Like palindromeArmLength, both palindromeLeftArm and palindromeRightArm will raise an error if x has no arms. Also, when applied to an XStringViews object x, both behave in a vectorized fashion by returning an XStringViews object of the same length as x.
像palindromeArmLength都palindromeLeftArm和palindromeRightArm将引发一个错误，如果x有没有武器。此外，当应用到一个XStringViews对象x，既表现在矢量时尚返回一个相同长度的xXStringViews对象。


作者（S）----------Author(s)----------


H. Pages



参见----------See Also----------

maskMotif, matchPattern, matchLRPatterns, matchProbePair, XStringViews-class, DNAString-class
maskMotif，matchPattern，matchLRPatterns，matchProbePair，级XStringViews，DNAString级


举例----------Examples----------


  ## Note that complemented palindromes (like palindromes) can be nested[＃注意补充回文（如回文）可以嵌套]
  findComplementedPalindromes(DNAString("ACGTTNAACGT-ACGTTNAACGT"))

  ## A real use case[＃实际使用情况]
  library(BSgenome.Dmelanogaster.UCSC.dm3)
  chrX <- Dmelanogaster$chrX
  chrX_pals <- findComplementedPalindromes(chrX, min.armlength=50, max.looplength=20)
  complementedPalindromeArmLength(chrX_pals)  # 251[251]

  ## Of course, whitespaces matter[＃当然，空格无所谓]
  palindromeArmLength(BString("was it a car or a cat I saw"))

  ## Note that the 2 arms of a strict palindrome (or strict complemented[＃需要注意的是严格的回文2武器（或严格的补充]
  ## palindrome) are equal to the full sequence.[＃回文）等于全序列。]
  palindromeLeftArm(BString("Delia saw I was aileD"))
  complementedPalindromeLeftArm(DNAString("N-ACGTT-AACGT-N"))
  palindromeLeftArm(DNAString("N-AAA-N-N-TTT-N"))

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


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