biodist r语言_R语言 Biostrings包 pairwiseAlignment()函数中文帮助文档(中英文对照)

pairwiseAlignment(Biostrings)

pairwiseAlignment()所属R语言包：Biostrings

Optimal Pairwise Alignment

最佳成对排列

译者：生物统计家园网 机器人LoveR

描述----------Description----------

Solves (Needleman-Wunsch) global alignment, (Smith-Waterman) local alignment, and (ends-free) overlap alignment problems.

解决(Needleman文施)全球对齐，(Smith-Waterman算法)地方对齐，(完)重叠对齐问题。

用法----------Usage----------

pairwiseAlignment(pattern, subject, ...)

## S4 method for signature 'XStringSet,XStringSet'

pairwiseAlignment(pattern, subject,

patternQuality = PhredQuality(22L), subjectQuality = PhredQuality(22L),

type = "global", substitutionMatrix = NULL, fuzzyMatrix = NULL,

gapOpening = -10, gapExtension = -4, scoreOnly = FALSE)

## S4 method for signature 'QualityScaledXStringSet,QualityScaledXStringSet'

pairwiseAlignment(pattern, subject,

type = "global", substitutionMatrix = NULL, fuzzyMatrix = NULL,

gapOpening = -10, gapExtension = -4, scoreOnly = FALSE)

参数----------Arguments----------

参数：pattern

a character vector of any length, an XString, or an XStringSet object.

一个任意长度的字符向量，：XString或XStringSet对象。

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：patternQuality, subjectQuality

objects of class XStringQuality representing the respective quality scores for pattern and subject that are used in a quality-based method for generating a substitution matrix. These two arguments are ignored if !is.null(substitutionMatrix) or if its respective string set (pattern, subject) is of class QualityScaledXStringSet.

类对象XStringQualitypattern和subject是为质量为基础的方法，产生一个置换矩阵代表各自的质量分数。这两个参数被忽略如果!is.null(substitutionMatrix)或者其各自的字符串集(pattern，subject)类QualityScaledXStringSet。

参数：type

type of alignment. O