srdistance(ShortRead)
srdistance()所属R语言包：ShortRead
Edit distances between reads and a small number of short references
编辑读取和短引用少数之间的距离
译者：生物统计家园网 机器人LoveR
描述----------Description----------
srdistance calculates the edit distance from each read in pattern to each read in subject. The underlying algorithm pairwiseAlignment is only efficient when both reads are short, and when the number of subject reads is small.
srdistance计算pattern的每读subject每次读取的编辑距离。底层算法pairwiseAlignment是唯一有效的，当两个读短，和subject读取数小时。
用法----------Usage----------
srdistance(pattern, subject, ...)
参数----------Arguments----------
参数：pattern
An object of class DNAStringSet containing reads whose edit distance is desired.
需要一个对象的类DNAStringSet含读的编辑距离。
参数：subject
A short character vector, DNAString or (small) DNAStringSet to serve as reference.
一个简短的character向量，DNAString（小）DNAStringSet作为参考。
参数：...
additional arguments, forward to srapply.
额外的参数，着srapply。
Details
详情----------Details----------
The underlying algorithm performs pairwise alignment from each read in pattern to each sequence in subject. The return value is a list of numeric vectors of distances, one list element for each sequence in subject. The vector in each list element contains for each read in pattern the edit distance from the read to the corresponding subject. The weight matrix and gap penalties used to calculate the distance are structured to weight base substitutions and single base insert/deletions equally. Edit distance between known and ambiguous (e.g., N) nucleotides, or between ambiguous nucleotides, are weighted as though each possible nucleotide in the ambiguity were equally likely.
底层算法执行每读patternsubject每个序列的两两对齐。返回值是一个数值向量的距离，每个序列列表subject元素的列表。在每个列表元素的向量包含每pattern从阅读到相应的主题编辑距离的读取。重量碱基和单碱基插入/缺失同样的结构，以用来计算距离的权重矩阵和差距处罚。编辑之间的距离已知的和模糊的（例如，N）的核苷酸，或暧昧核苷酸之间，仿佛每一个可能的核苷酸中的模糊加权同样可能。
值----------Value----------
A list of length equal to that of subject. Each element is a numeric vector equal to the length of pattern, with values corresponding to the minimum distance between between the corresponding pattern and subject sequences.
长度等于subject名单。 pattern长度值之间的对应模式和主题序列之间的最小距离，等于每个元素都是一个数值向量。
作者（S）----------Author(s)----------
Martin Morgan <mtmorgan@fhcrc.org>
参见----------See Also----------
pairwiseAlignment
pairwiseAlignment
举例----------Examples----------
sp <- SolexaPath(system.file("extdata", package="ShortRead"))
aln <- readAligned(sp, "s_2_export.txt")
polyA <- polyn("A", 35)
polyT <- polyn("T", 35)
d1 <- srdistance(clean(sread(aln)), polyA)
d2 <- srdistance(sread(aln), polyA)
d3 <- srdistance(sread(aln), c(polyA, polyT))
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 2012-2-26 14:09:29
