PairwiseAlignedXStringSet-class(Biostrings)
PairwiseAlignedXStringSet-class()所属R语言包：Biostrings
PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and
PairwiseAlignedXStringSet，PairwiseAlignedFixedSubject，
译者：生物统计家园网 机器人LoveR
描述----------Description----------
The PairwiseAlignedXStringSet class is a container for storing an elementwise pairwise alignment. The PairwiseAlignedFixedSubject class is a container for storing a pairwise alignment with a single subject. The PairwiseAlignedFixedSubjectSummary class is a container for storing the summary of an alignment.
PairwiseAlignedXStringSet类是一个用于存储的elementwise成对排列的集装箱。 类PairwiseAlignedFixedSubject存储成对对齐，用一个单一的主题是一个容器。 类PairwiseAlignedFixedSubjectSummary是一个容器，用于存储对齐总结。
用法----------Usage----------
## Constructors:
## When subject is missing, pattern must be of length 2
## S4 method for signature 'XString,XString'
PairwiseAlignedXStringSet(pattern, subject,
type = "global", substitutionMatrix = NULL, gapOpening = 0, gapExtension = -1)
## S4 method for signature 'XStringSet,missing'
PairwiseAlignedXStringSet(pattern, subject,
type = "global", substitutionMatrix = NULL, gapOpening = 0, gapExtension = -1)
## S4 method for signature 'character,character'
PairwiseAlignedXStringSet(pattern, subject,
type = "global", substitutionMatrix = NULL, gapOpening = 0, gapExtension = -1,
baseClass = "BString")
## S4 method for signature 'character,missing'
PairwiseAlignedXStringSet(pattern, subject,
type = "global", substitutionMatrix = NULL, gapOpening = 0, gapExtension = -1,
baseClass = "BString")
参数----------Arguments----------
参数：pattern
a character vector of length 1 or 2, an XString, or an XStringSet object of length 1 or 2.
特征向量的长度为1或2，XString或XStringSet对象的长度为1或2。
参数：subject
a character vector of length 1 or an XString object.
一个字符长度为1的或XString对象的向量。
参数：type
type of alignment. One of "global", "local", "overlap", "global-local", and "local-global" where "global" = align whole strings with end gap penalties, "local" = align string fragments, "overlap" = align whole strings without end gap penalties, "global-local" = align whole strings in pattern with consecutive subsequence of subject, "local-global" = align consecutive subsequence of pattern with whole strings in subject.
对齐类型。 "global"，"local"，"overlap"，"global-local"，"local-global"其中"global"=对齐结尾差距处罚的整个字符串，<X >=对齐字符串碎片，"local"=调整没有结束的差距处罚的整个字符串，"overlap"=对齐整个字符串"global-local"pattern，subject连续序列=对齐连续序列"local-global"与pattern整个字符串。
参数：substitutionMatrix
substitution matrix for the alignment. If NULL, the diagonal values and off-diagonal values are set to 0 and 1 respectively.
替代矩阵对齐。如果为NULL，对角线值和非对角线的值分别设置为0和1。
参数：gapOpening
the cost for opening a gap in the alignment.
成本开放对齐的差距。
参数：gapExtension
the incremental cost incurred along the length of the gap in the alignment.
沿长度对齐的差距产生的增量成本。
参数：baseClass
the base XString class to use in the alignment.
碱基XString类使用对齐。
Details
详情----------Details----------
Before we define the notion of alignment, we introduce the notion of "filled-with-gaps subsequence". A "filled-with-gaps subsequence" of a string string1 is obtained by inserting 0 or any number of gaps in a subsequence of s1. For example L-A–ND and A–N-D are "filled-with-gaps subsequences" of LAND. An alignment between two strings string1 and string2 results in two strings (align1 and align2) that have the same length and are "filled-with-gaps subsequences" of string1 and string2.
我们定义对齐的概念之前，我们引进“的差距，填补与序列”的概念。一个“隙填充与序列”的字符串string1中获得通过插入0或任何数量的差距在S1的序列。例如L-A-Nd和A-ND折价“的差距，填补与子序列”的土地。两个字符串string1和string2两个字符串（align1和align2），有相同的长度和“填写与差距子序列”string1和string2的结果之间的对齐。
For example, this is an alignment between LAND and LEAVES:
举例来说，这是一个土地和树叶之间的对齐：
对象提取方法----------Object extraction methods----------
In the code snippets below, x is a PairwiseAlignedXStringSet object, except otherwise noted.
在下面的代码片段，x是PairwiseAlignedXStringSet对象，除另有注明。
pattern(x): The AlignedXStringSet object for the pattern.
pattern(x)：AlignedXStringSet模式的对象。
subject(x): The AlignedXStringSet object for the subject.
subject(x)：AlignedXStringSet为主题的对象。
summary(object, ...): Generates a summary for the PairwiseAlignedXStringSet.
summary(object, ...)：生成为PairwiseAlignedXStringSet总结。
一般信息的方法----------General information methods----------
In the code snippets below, x is a PairwiseAlignedXStringSet object, except otherwise noted.
在下面的代码片段，x是PairwiseAlignedXStringSet对象，除另有注明。
alphabet(x): Equivalent to alphabet(unaligned(subject(x))).
alphabet(x)：alphabet(unaligned(subject(x)))等效。
length(x): The length of the aligned(pattern(x)) and aligned(subject(x)). There is a method for PairwiseAlignedFixedSubjectSummary as well.
length(x)：aligned(pattern(x))和aligned(subject(x))的长度。 PairwiseAlignedFixedSubjectSummary以及有一个方法。
type(x): The type of the alignment ("global", "local", "overlap", "global-local", or "local-global"). There is a method for PairwiseAlignedFixedSubjectSummary as well.
type(x)：对齐类型（"global"，"local"，"overlap"，"global-local"或"local-global"）。 PairwiseAlignedFixedSubjectSummary以及有一个方法。
不结盟序列方法----------Aligned sequence methods----------
In the code snippets below, x is a PairwiseAlignedFixedSubject object, except otherwise noted.
在下面的代码片段，x是PairwiseAlignedFixedSubject对象，除另有注明。
aligned(x, degap = FALSE, gapCode="-", endgapCode="-"): If degap = FALSE, "align" the alignments by returning an XStringSet object containing the aligned patterns without insertions. If degap = TRUE, returns aligned(pattern(x), degap=TRUE). The gapCode and endgapCode arguments denote the code in the appropriate alphabet to use for the internal and end gaps.
aligned(x, degap = FALSE, gapCode="-", endgapCode="-")如果degap = FALSE，“对齐”的路线，通过返回一个XStringSet对象，其中包含没有插入，对齐模式。如果degap = TRUE，回报aligned(pattern(x), degap=TRUE)。 gapCode和endgapCode参数表示在适当的alphabet代码用于内部和结束的差距。
as.character(x): Converts aligned(x) to a character vector.
as.character(x)：aligned(x)字符向量转换。
as.matrix(x): Returns an "exploded" character matrix representation of aligned(x).
as.matrix(x)：返回一个“爆炸”aligned(x)字符矩阵表示。
toString(x): Equivalent to toString(as.character(x)).
toString(x)：toString(as.character(x))等效。
主题位置的方法----------Subject position methods----------
In the code snippets below, x is a PairwiseAlignedFixedSubject object, except otherwise noted.
在下面的代码片段，x是PairwiseAlignedFixedSubject对象，除另有注明。
consensusMatrix(x, as.prob=FALSE, baseOnly=FALSE, gapCode="-", endgapCode="-") See 'consensusMatrix' for more information.
consensusMatrix(x, as.prob=FALSE, baseOnly=FALSE, gapCode="-", endgapCode="-")更多信息，请参阅“consensusMatrix”。
consensusString(x) See 'consensusString' for more information.
consensusString(x)见consensusString更多信息。
coverage(x, shift=0L, width=NULL, weight=1L) See 'coverage,PairwiseAlignedFixedSubject-method' for more information.
coverage(x, shift=0L, width=NULL, weight=1L)更多信息，请参阅“报道，PairwiseAlignedFixedSubject法”。
Views(subject, start=NULL, end=NULL, width=NULL, names=NULL): The XStringViews object that represents the pairwise alignments along unaligned(subject(subject)). The start and end arguments must be either NULL/NA or an integer vector of length 1 that denotes the offset from start(subject(subject)).
Views(subject, start=NULL, end=NULL, width=NULL, names=NULL)：XStringViews对象，表示沿unaligned(subject(subject))成对路线。 start和end参数必须是要么NULL/NA或向量的长度为1的整数，表示从start(subject(subject))抵销。
数字汇总方法----------Numeric summary methods----------
In the code snippets below, x is a PairwiseAlignedXStringSet object, except otherwise noted.
在下面的代码片段，x是PairwiseAlignedXStringSet对象，除另有注明。
nchar(x): The nchar of the aligned(pattern(x)) and aligned(subject(x)). There is a method for PairwiseAlignedFixedSubjectSummary as well.
nchar(x)：aligned(pattern(x))和aligned(subject(x))NCHAR。 PairwiseAlignedFixedSubjectSummary以及有一个方法。
insertion(x): An CompressedIRangesList object containing the locations of the insertions from the perspective of the pattern.
insertion(x)：CompressedIRangesList对象包含从pattern的角度的插入位置。
deletion(x): An CompressedIRangesList object containing the locations of the deletions from the perspective of the pattern.
deletion(x)：CompressedIRangesList对象包含从pattern的角度的缺失的位置。
indel(x): An InDel object containing the locations of the insertions and deletions from the perspective of the pattern.
indel(x)：InDel对象含有从pattern的角度插入和缺失的位置的。
nindel(x): An InDel object containing the number of insertions and deletions.
nindel(x)：InDel对象，其中包含插入和删除。
score(x): The score of the alignment. There is a method for PairwiseAlignedFixedSubjectSummary as well.
score(x)：对齐的得分。 PairwiseAlignedFixedSubjectSummary以及有一个方法。
子集的方法----------Subsetting methods----------
x[i]: Returns a new PairwiseAlignedXStringSet object made of the selected elements.
x[i]：返回一个新的PairwiseAlignedXStringSet对象选定的元素。
rep(x, times): Returns a new PairwiseAlignedXStringSet object made of the repeated elements.
rep(x, times)：返回一个新的PairwiseAlignedXStringSet对象反复元素制成。
作者（S）----------Author(s)----------
P. Aboyoun
参见----------See Also----------
pairwiseAlignment, AlignedXStringSet-class, XString-class, XStringViews-class, align-utils, pid
pairwiseAlignment，AlignedXStringSet-class，XString-class，XStringViews-class，align-utils，pid
举例----------Examples----------
PairwiseAlignedXStringSet("-PA--W-HEAE", "HEAGAWGHE-E")
pattern <- AAStringSet(c("HLDNLKGTF", "HVDDMPNAL"))
subject <- AAString("SMDDTEKMSMKL")
nw1 <- pairwiseAlignment(pattern, subject, substitutionMatrix = "BLOSUM50",
gapOpening = -3, gapExtension = -1)
pattern(nw1)
subject(nw1)
aligned(nw1)
as.character(nw1)
as.matrix(nw1)
nchar(nw1)
score(nw1)
nw1
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注：
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发表于 2012-2-25 13:48:28
