matchProbePair(Biostrings)
matchProbePair()所属R语言包：Biostrings
Find "theoretical amplicons" mapped to a probe pair
查找映射到一个探针对“理论扩增”
译者：生物统计家园网 机器人LoveR
描述----------Description----------
In the context of a computer-simulated PCR experiment, one wants to find the amplicons mapped to a given primer pair. The matchProbePair function can be used for this: given a forward and a reverse probe (i.e. the chromosome-specific sequences of the forward and reverse primers used for the experiment) and a target sequence (generally a chromosome sequence), the matchProbePair function will return all the "theoretical amplicons" mapped to this probe pair.
在计算机模拟PCR实验的情况下，要找到映射到一个给定的引物扩增。 matchProbePair函数可以用于：正向和反向探针（即正向和反向引物，用于实验的特定染色体的序列）和目标（通常是一个染色体序列）序列， matchProbePair函数将返回所有“理论映射到该探针对扩增”。
用法----------Usage----------
matchProbePair(Fprobe, Rprobe, subject, algorithm="auto", logfile=NULL, verbose=FALSE)
参数----------Arguments----------
参数：Fprobe
The forward probe.
向前探针。
参数：Rprobe
The reverse probe.
反向探针。
参数：subject
A DNAString object (or an XStringViews object with a DNAString subject) containing the target sequence.
一个DNAString对象（或XStringViews主体对象DNAString）含有靶序列。
参数：algorithm
One of the following: "auto", "naive-exact", "naive-inexact", "boyer-moore" or "shift-or". See matchPattern for more information.
下列操作之一："auto"，"naive-exact"，"naive-inexact"，"boyer-moore"或"shift-or"。看到matchPattern更多信息。
参数：logfile
A file used for logging.
一个文件用于记录。
参数：verbose
TRUE or FALSE.
TRUE或FALSE。
Details
详情----------Details----------
The matchProbePair function does the following: (1) find all the "plus hits" i.e. the Fprobe and Rprobe matches on the "plus" strand, (2) find all the "minus hits" i.e. the Fprobe and Rprobe matches on the "minus" strand and (3) from the set of all (plus\_hit, minus\_hit) pairs, extract and return the subset of "reduced matches" i.e. the (plus\_hit, minus\_hit) pairs such that (a) plus\_hit <= minus\_hit and (b) there are no hits (plus or minus) between plus\_hit and minus\_hit. This set of "reduced matches" is the set of "theoretical amplicons".
matchProbePair函数执行以下操作：（1）找到所有的“加命中”上“加”链，即Fprobe和Rprobe比赛，（2）找到所有的“减去命中”Fprobe即“减”链（3）所有（加\ _hit，减\ _hit）对Rprobe比赛，提取和返回（加\ _hit“减少比赛”，即子集，减去\这样_hit）对（一）加\ _hit <=减去\ _hit及（b）有没有命中（加上或减去）之间加\ _hit和零下\ _hit的的。这一套“减少匹配”是一套“理论扩增”。
值----------Value----------
An XStringViews object containing the set of "theoretical amplicons".
一个XStringViews对象，它包含了一套“理论扩增”。
作者（S）----------Author(s)----------
H. Pages
参见----------See Also----------
matchPattern, matchLRPatterns, findPalindromes, reverseComplement, XStringViews
matchPattern，matchLRPatterns，findPalindromes，reverseComplement，XStringViews
举例----------Examples----------
library(BSgenome.Dmelanogaster.UCSC.dm3)
subject <- Dmelanogaster$chr3R
## With 20-nucleotide forward and reverse probes:[＃20核苷酸的正向和反向探针：]
Fprobe <- "AGCTCCGAGTTCCTGCAATA"
Rprobe <- "CGTTGTTCACAAATATGCGG"
matchProbePair(Fprobe, Rprobe, subject) # 1 "theoretical amplicon"[1“的理论扩增”]
## With shorter forward and reverse probes, the risk of having multiple[＃短的正向和反向探针，有多个风险]
## "theoretical amplicons" increases:[＃“理论扩增”增加：]
Fprobe <- "AGCTCCGAGTTCC"
Rprobe <- "CGTTGTTCACAA"
matchProbePair(Fprobe, Rprobe, subject) # 2 "theoretical amplicons"[2“的理论扩增”]
Fprobe <- "AGCTCCGAGTT"
Rprobe <- "CGTTGTTCACA"
matchProbePair(Fprobe, Rprobe, subject) # 9 "theoretical amplicons"[9“理论扩增”]
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。
|
发表于 2012-2-25 13:47:20
