reverseComplement(Biostrings)
reverseComplement()所属R语言包：Biostrings
Sequence reversing and complementing
倒车和互补序列
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Use these functions for reversing sequences and/or complementing DNA or RNA sequences.
扭转序列和/或互补的DNA或RNA序列，使用这些功能。
用法----------Usage----------
complement(x, ...)
reverseComplement(x, ...)
参数----------Arguments----------
参数：x
A DNAString, RNAString, DNAStringSet, RNAStringSet, XStringViews (with DNAString or RNAString subject), MaskedDNAString or MaskedRNAString object for complement and reverseComplement.
一个DNAString，RNAString，DNAStringSet，RNAStringSet，XStringViews与DNAString或RNAString主题，MaskedDNAString或MaskedRNAStringcomplement和reverseComplement对象。
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----------
See ?reverse for reversing an XString, XStringSet or XStringViews object.
看到?reverse扭转一个XString，XStringSet或XStringViews对象。
If x is a DNAString or RNAString object, complement(x) returns an object where each base in x is "complemented" i.e. A, C, G, T in a DNAString object are replaced by T, G, C, A respectively and A, C, G, U in a RNAString object are replaced by U, G, C, A respectively.
如果x是DNAString或RNAString对象，complement(x)返回一个每个x碱基“补充”对象，即A，C，G，T在DNAString对象所取代T，G，A分别与A，C，Gü在RNAString对象是由U，G，C，A分别取代。
Letters belonging to the IUPAC Extended Genetic Alphabet are also replaced by their complement (M <-> K, R <-> Y, S <-> S, V <-> B, W <-> W, H <-> D, N <-> N) and the gap ("-") and hard masking ("+") letters are unchanged.
信件也属于扩展的遗传字母的IUPAC取代的补（男< - > K，R < - > Y，< - > S，V] < - >乙，宽< - >宽，高< - > D，氮< - > N）和差距（"-"）和硬掩蔽（"+"）字母是不变的。
reverseComplement(x) is equivalent to reverse(complement(x)) but is faster and more memory efficient.
reverseComplement(x)相当于reverse(complement(x))的，而且是更快和更高效的内存。
值----------Value----------
An object of the same class and length as the original object.
同一类的对象和原始对象的长度。
参见----------See Also----------
reverse, DNAString-class, RNAString-class, DNAStringSet-class, RNAStringSet-class, XStringViews-class, MaskedXString-class, chartr, findPalindromes, IUPAC_CODE_MAP
相反，DNAString类，级RNAString，级DNAStringSet，级RNAStringSet，级XStringViews，MaskedXString级，chartr，findPalindromes，IUPAC_CODE_MAP
举例----------Examples----------
## ---------------------------------------------------------------------[＃------------------------------------------------- --------------------]
## A. SOME SIMPLE EXAMPLES[＃答：一些简单的例子]
## ---------------------------------------------------------------------[＃------------------------------------------------- --------------------]
x <- DNAString("ACGT-YN-")
reverseComplement(x)
library(drosophila2probe)
probes <- DNAStringSet(drosophila2probe)
probes
alphabetFrequency(probes, collapse=TRUE)
rcprobes <- reverseComplement(probes)
rcprobes
alphabetFrequency(rcprobes, collapse=TRUE)
## ---------------------------------------------------------------------[＃------------------------------------------------- --------------------]
## B. OBTAINING THE MISMATCH PROBES OF A CHIP[＃B.获取芯片不匹配探针]
## ---------------------------------------------------------------------[＃------------------------------------------------- --------------------]
pm2mm <- function(probes)
{
probes <- DNAStringSet(probes)
subseq(probes, start=13, end=13) <- complement(subseq(probes, start=13, end=13))
probes
}
mmprobes <- pm2mm(probes)
mmprobes
alphabetFrequency(mmprobes, collapse=TRUE)
## ---------------------------------------------------------------------[＃------------------------------------------------- --------------------]
## C. SEARCHING THE MINUS STRAND OF A CHROMOSOME[＃C.搜索染色体的负链]
## ---------------------------------------------------------------------[＃------------------------------------------------- --------------------]
## Applying reverseComplement() to the pattern before calling[＃在应用reverseComplement（）之前调用模式]
## matchPattern() is the recommended way of searching hits on the[，＃matchPattern（）是推荐的方式上的搜索点击]
## minus strand of a chromosome.[＃染色体的负链。]
library(BSgenome.Dmelanogaster.UCSC.dm3)
chrX <- Dmelanogaster$chrX
pattern <- DNAString("ACCAACNNGGTTG")
matchPattern(pattern, chrX, fixed=FALSE) # 3 hits on strand +[3点击上链+]
rcpattern <- reverseComplement(pattern)
rcpattern
m0 <- matchPattern(rcpattern, chrX, fixed=FALSE)
m0 # 5 hits on strand -[5链命中 - ]
## Applying reverseComplement() to the subject instead of the pattern is not[＃在应用reverseComplement（）的格局，而不是问题不]
## a good idea for 2 reasons:[＃一个好主意，原因有二：]
## (1) Chromosome sequences are generally big and sometimes very big[＃（1）染色体序列是一般大，有时是非常大的]
## so computing the reverse complement of the positive strand will[＃所以计算正股反向补]
## take time and memory proportional to its length.[＃需要时间和内存长度成正比。]
chrXminus <- reverseComplement(chrX) # needs to allocate 22M of memory![需要分配22M内存！]
chrXminus
## (2) Chromosome locations are generally given relatively to the positive[＃（2）染色体的位置一般都相对积极]
## strand, even for features located in the negative strand, so after[＃链，即使是在位于负链的特性，所以后]
## doing this:[＃做这个：]
m1 <- matchPattern(pattern, chrXminus, fixed=FALSE)
## the start/end of the matches are now relative to the negative strand.[＃开始/结束的比赛是相对负链。]
## You need to apply reverseComplement() again on the result if you want[＃你需要再次申请结果reverseComplement（）如果你想]
## them to be relative to the positive strand:[＃它们是相对于正股：]
m2 <- reverseComplement(m1) # allocates 22M of memory, again![分配22M内存，再次！]
## and finally to apply rev() to sort the matches from left to right[＃终于申请转（）的比赛进行排序从左至右]
## (5'3' direction) like in m0:[＃（53方向），如在M0：]
m3 <- rev(m2) # same as m0, finally![同为M0，终于来了！]
## WARNING: Before you try the example below on human chromosome 1, be aware[＃警告：您尝试之前人类1号染色体上下面的例子中，要注意]
## that it will require the allocation of about 500Mb of memory![＃这将需要约500MB的内存分配！]
if (interactive()) {
library(BSgenome.Hsapiens.UCSC.hg18)
chr1 <- Hsapiens$chr1
matchPattern(pattern, reverseComplement(chr1)) # DON'T DO THIS![千万不要这样做！]
matchPattern(reverseComplement(pattern), chr1) # DO THIS INSTEAD[做，而不是]
}
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。
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发表于 2012-2-25 13:49:32
