align-utils(Biostrings)
align-utils()所属R语言包：Biostrings
Utility functions related to sequence alignment
相关的序列比对的实用功能
译者：生物统计家园网 机器人LoveR
描述----------Description----------
A variety of different functions used to deal with sequence alignments.
各种不同的功能用于处理序列比对。
用法----------Usage----------
nedit(x) # also nmatch and nmismatch
mismatchTable(x, shiftLeft=0L, shiftRight=0L, ...)
mismatchSummary(x, ...)
## S4 method for signature 'AlignedXStringSet0'
coverage(x, shift=0L, width=NULL, weight=1L)
## S4 method for signature 'PairwiseAlignedFixedSubject'
coverage(x, shift=0L, width=NULL, weight=1L)
compareStrings(pattern, subject)
## S4 method for signature 'PairwiseAlignedFixedSubject'
consensusMatrix(x,
as.prob=FALSE, shift=0L, width=NULL,
baseOnly=FALSE, gapCode="-", endgapCode="-")
参数----------Arguments----------
参数：x
A character vector or matrix, XStringSet, XStringViews, PairwiseAlignedXStringSet, or list of FASTA records containing the equal-length strings.
一个character向量或矩阵，XStringSet，XStringViews，PairwiseAlignedXStringSet或listFASTA格式的记录包含相等长度的字符串。
参数：shiftLeft, shiftRight
Non-positive and non-negative integers respectively that specify how many preceding and succeeding characters to and from the mismatch position to include in the mismatch substrings.
非正非负整数分别指定多少前和成功的和不匹配的位置，包括在不匹配的子串的字符。
参数：...
Further arguments to be passed to or from other methods.
进一步的参数被传递或其他方法。
参数：shift, width
See ?coverage.
看到?coverage。
参数：weight
An integer vector specifying how much each element in x counts.
指定一个整数向量多少x计数的每个元素。
参数：pattern, subject
The strings to compare. Can be of type character, XString, XStringSet, AlignedXStringSet, or, in the case of pattern, PairwiseAlignedXStringSet. If pattern is a PairwiseAlignedXStringSet object, then subject must be missing.
字符串比较。类型可以character，XString，XStringSet，AlignedXStringSet，或在pattern，PairwiseAlignedXStringSet的情况。 pattern如果是PairwiseAlignedXStringSet对象，然后subject必须是失踪。
参数：as.prob
If TRUE then probabilities are reported, otherwise counts (the default).
如果TRUE然后概率报道，否则计数（默认）。
参数：baseOnly
TRUE or FALSE. If TRUE, the returned vector only contains frequencies for the letters in the "base" alphabet i.e. "A", "C", "G", "T" if x is a "DNA input", and "A", "C", "G", "U" if x is "RNA input". When x is a BString object (or an XStringViews object with a BString subject, or a BStringSet object), then the baseOnly argument is ignored.
TRUE或FALSE。如果TRUE，返回向量只包含字母，即“碱基”的字母“A”，“C”，“G”的，“T”型的频率，如果x “DNA输入”，“A”“C”的“G”，“U”型x如果是“核糖核酸输入”。当x是一个BString对象（或与BString主题XStringViews对象，或BStringSet对象），然后baseOnly参数将被忽略。
参数：gapCode, endgapCode
The codes in the appropriate alphabet to use for the internal and end gaps.
在代码相应的alphabet用于内部和结束的差距。
Details
详情----------Details----------
mismatchTable: a data.frame containing the positions and substrings of the mismatches for the AlignedXStringSet or PairwiseAlignedXStringSet object.
mismatchTable：数据框包含AlignedXStringSet或PairwiseAlignedXStringSet对象的立场和不匹配的子串。
mismatchSummary: a list of data.frame objects containing counts and frequencies of the mismatches for the AlignedXStringSet or PairwiseAlignedFixedSubject object.
mismatchSummary：包含AlignedXStringSet或PairwiseAlignedFixedSubject对象的数量和频率的不匹配数据框对象名单。
compareStrings combines two equal-length strings that are assumed to be aligned into a single character string containing that replaces mismatches with "?", insertions with "+", and deletions with "-".
compareStrings结合两个相等的长度被假定为对齐到一个单一的字符，包含字符串替换"?"，"+"，"-"删除插入的不匹配的字符串。
参见----------See Also----------
pairwiseAlignment, consensusMatrix, XString-class, XStringSet-class, XStringViews-class, AlignedXStringSet-class, PairwiseAlignedXStringSet-class, match-utils
pairwiseAlignment，consensusMatrix，级XStringViews，级XStringSet，XString-级，级AlignedXStringSet，级PairwiseAlignedXStringSet，比赛-utils的
举例----------Examples----------
## Compare two globally aligned strings[＃比较两个字符串，全球一致。]
string1 <- "ACTTCACCAGCTCCCTGGCGGTAAGTTGATC---AAAGG---AAACGCAAAGTTTTCAAG"
string2 <- "GTTTCACTACTTCCTTTCGGGTAAGTAAATATATAAATATATAAAAATATAATTTTCATC"
compareStrings(string1, string2)
## Create a consensus matrix[＃创建一个共识矩阵]
nw1 <-
pairwiseAlignment(AAStringSet(c("HLDNLKGTF", "HVDDMPNAL")), AAString("SMDDTEKMSMKL"),
substitutionMatrix = "BLOSUM50", gapOpening = -3, gapExtension = -1)
consensusMatrix(nw1)
## Examine the consensus between the bacteriophage phi X174 genomes[＃检查披X174噬菌体基因组之间的共识。]
data(phiX174Phage)
phageConsmat <- consensusMatrix(phiX174Phage, baseOnly = TRUE)
phageDiffs <- which(apply(phageConsmat, 2, max) < length(phiX174Phage))
phageDiffs
phageConsmat[,phageDiffs]
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 2012-2-25 13:43:29
