match-utils(Biostrings)
match-utils()所属R语言包:Biostrings
Utility functions operating on the matches returned by a
返回的比赛经营的实用功能
译者:生物统计家园网 机器人LoveR
描述----------Description----------
Miscellaneous utility functions operating on the matches returned by a high-level matching function like matchPattern, matchPDict, etc...
杂项实用功能上由一个高层次的匹配像matchPattern,matchPDict等功能返回的匹配操作......
用法----------Usage----------
mismatch(pattern, x, fixed=TRUE)
nmatch(pattern, x, fixed=TRUE)
nmismatch(pattern, x, fixed=TRUE)
## S4 method for signature 'MIndex'
coverage(x, shift=0L, width=NULL, weight=1L)
## S4 method for signature 'MaskedXString'
coverage(x, shift=0L, width=NULL, weight=1L)
参数----------Arguments----------
参数:pattern
The pattern string.
模式字符串。
参数:x
An XStringViews object for mismatch (typically, one returned by matchPattern(pattern, subject)). An MIndex object for coverage, or any object for which a coverage method is defined. See ?coverage.
一个XStringViews对象mismatch(通常情况下,matchPattern(pattern, subject)返回)。一个coverage或coverage方法被定义为任何对象MIndex对象。看到?coverage。
参数:fixed
See ?`lowlevel-matching`.
看到?lowlevel-matching。
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。
Details
详情----------Details----------
The mismatch function gives the positions of the mismatching letters of a given pattern relatively to its matches in a given subject.
mismatch功能提供了一个给定的模式在特定主题的比赛相对不匹配字母的位置。
The nmatch and nmismatch functions give the number of matching and mismatching letters produced by the mismatch function.
nmatch和nmismatch功能给予匹配和不匹配mismatch函数的信件数量。
The coverage function computes the "coverage" of a subject by a given pattern or set of patterns.
coverage函数计算一个给定的模式或一套模式“覆盖”的主题。
值----------Value----------
mismatch: a list of integer vectors.
mismatch:整数向量列表。
nmismatch: an integer vector containing the length of the vectors produced by mismatch.
nmismatch:整数向量由mismatch产生的向量长度。
coverage: an Rle object indicating the coverage of x. See ?coverage for the details. If x is an MIndex object, the coverage of a given position in the underlying sequence (typically the subject used during the search that returned x) is the number of matches (or hits) it belongs to.
coverage:一个RLE对象表示x的覆盖面。看到?coverage细节。如果x是MIndex的对象,覆盖底层序列在给定的位置(通常返回在搜索过程中使用的主题x)是比赛的数量(或点击),它属于。
参见----------See Also----------
lowlevel-matching, matchPattern, matchPDict, XString-class, XStringViews-class, MIndex-class, coverage, align-utils
低级匹配,matchPattern,matchPDict,一流XString,XStringViews级,MIndex类,覆盖,对齐-utils的
举例----------Examples----------
## ---------------------------------------------------------------------[#------------------------------------------------- --------------------]
## mismatch() / nmismatch()[#不匹配()/ nmismatch()]
## ---------------------------------------------------------------------[#------------------------------------------------- --------------------]
subject <- DNAString("ACGTGCA")
m <- matchPattern("NCA", subject, max.mismatch=1, fixed=FALSE)
mismatch("NCA", m)
nmismatch("NCA", m)
## ---------------------------------------------------------------------[#------------------------------------------------- --------------------]
## coverage()[#覆盖率()]
## ---------------------------------------------------------------------[#------------------------------------------------- --------------------]
coverage(m)
## See ?matchPDict for examples of using coverage() on an MIndex object...[#看到了吗?使用上MIndex对象覆盖()的例子matchPDict ...]
转载请注明:出自 生物统计家园网(http://www.biostatistic.net)。
注:
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