AlignedXStringSet-class(Biostrings)
AlignedXStringSet-class()所属R语言包:Biostrings
AlignedXStringSet and QualityAlignedXStringSet objects
AlignedXStringSet和QualityAlignedXStringSet对象
译者:生物统计家园网 机器人LoveR
描述----------Description----------
The AlignedXStringSet and QualityAlignedXStringSet classes are containers for storing an aligned XStringSet.
AlignedXStringSet和QualityAlignedXStringSet类容器储存对齐XStringSet。
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:
存取方法----------Accessor methods----------
In the code snippets below, x is a AlignedXStringSet or QualityAlignedXStringSet object.
在下面的代码片段,x是AlignedXStringSet或QualityAlignedXStringSet对象。
unaligned(x): The original string.
unaligned(x):原始字符串。
aligned(x, degap = FALSE): If degap = FALSE, the "filled-with-gaps subsequence" representing the aligned substring. If degap = TRUE, the "gap-less subsequence" representing the aligned substring.
aligned(x, degap = FALSE):如果degap = FALSE,“充满与空白序列”代表的一致的子串。如果degap = TRUE,“无间隙序列”代表的一致的子串。
start(x): The start of the aligned substring.
start(x):对齐子串的开始。
end(x): The end of the aligned substring.
end(x):对齐的子结束。
width(x): The width of the aligned substring, ignoring gaps.
width(x):对齐子串的宽度,无视差距。
indel(x): The positions, in the form of an IRanges object, of the insertions or deletions (depending on what x represents).
indel(x):职位,在IRanges对象的形式插入或缺失(取决于什么x代表),。
nindel(x): A two-column matrix containing the length and sum of the widths for each of the elements returned by indel.
nindel(x):返回一个两列的矩阵,包含的长度和每个元素的宽度的总和indel。
length(x): The length of the aligned(x).
length(x):的aligned(x)长度。
nchar(x): The nchar of the aligned(x).
nchar(x):aligned(x)NCHAR。
alphabet(x): Equivalent to alphabet(unaligned(x)).
alphabet(x):alphabet(unaligned(x))等效。
as.character(x): Converts aligned(x) to a character vector.
as.character(x):aligned(x)字符向量转换。
toString(x): Equivalent to toString(as.character(x)).
toString(x):toString(as.character(x))等效。
子集的方法----------Subsetting methods----------
x[i]: Returns a new AlignedXStringSet or QualityAlignedXStringSet object made of the selected elements.
x[i]:返回一个新的AlignedXStringSet或QualityAlignedXStringSet对象选定的元素。
rep(x, times): Returns a new AlignedXStringSet or QualityAlignedXStringSet object made of the repeated elements.
rep(x, times):返回一个新的AlignedXStringSet或QualityAlignedXStringSet对象反复元素制成。
作者(S)----------Author(s)----------
P. Aboyoun and H. Pages
参见----------See Also----------
pairwiseAlignment, PairwiseAlignedXStringSet-class, XStringSet-class
pairwiseAlignment,PairwiseAlignedXStringSet-class,XStringSet-class
举例----------Examples----------
pattern <- AAString("LAND")
subject <- AAString("LEAVES")
nw1 <- pairwiseAlignment(pattern, subject, substitutionMatrix = "BLOSUM50", gapOpening = -3, gapExtension = -1)
alignedPattern <- pattern(nw1)
unaligned(alignedPattern)
aligned(alignedPattern)
as.character(alignedPattern)
nchar(alignedPattern)
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注:
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