R语言 seqRFLP包 seqRFLP-package()函数中文帮助文档(中英文对照)

loveR

seqRFLP-package(seqRFLP)
seqRFLP-package()所属R语言包：seqRFLP

                                        Simulation and visualization of Restriction Fragment Length Polymorphism(RFLP) pattern from DNA sequences
                                         从DNA序列的限制性片段长度多态性（RFLP）模式的模拟和可视化

                                         译者：生物统计家园网 机器人LoveR

描述----------Description----------

This package includes functions for handling DNA sequences, especially for simulating RFLP and TRFLP pattern based on selected restriction enzyme and DNA sequences.
这个软件包包括处理DNA序列，特别是模拟的RFLP和TRFLP的模式的基础上选定的限制性内切酶和DNA序列的功能。


Details

详细信息----------Details----------

</table>
</ TABLE>


（作者）----------Author(s)----------



Qiong Ding <a href="mailto:dingqiong1@gmail.com">dingqiong1@gmail.com</a>
Jinlong zhang <a href="mailto:jinlongzhang01@gmail.com">jinlongzhang01@gmail.com</a>


Maintainer: Qiong Ding <a href="mailto:dingqiong1@gmail.com">dingqiong1@gmail.com</a>






参考文献----------References----------


Saiki RK, Scharf S, Faloona F, Mullis KB, Erlich HA, Arnheim N (1985). Enzymatic amplification of beta-globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia. Science 230 (4723):1350-4


实例----------Examples----------



### Featured examples[＃＃特色的例子]
### 1. File(s) importing:[＃＃1。进口文件（S）：]

### 1.1 importing fasta files.[＃＃1.1中导入fasta格式的文件。]
### read.fasta() example[＃：＃read.fasta（）的例子]
### [＃＃]
cat(
">No305",
"NTTCGAAAAACACACCCACTACTAAAANTTATCAGTCACT",
file = "dna1.fas", sep = "\n")
sequences <- read.fasta("dna1.fas")
unlink("dna1.fas")


### 1.2 Concatenating all fasta files in working directory to fasta data[＃＃1.2串联工作目录下的所有fasta格式的fasta格式的数据]
### raw2Fas() example[＃＃raw2Fas（）的例子]
cat(
">No305",
"NTTCGAAAAACACACCCACTACTAAAANTTATCAGTCACT",
file = "dna1.fas", sep = "\n")
cat(
">No304",
"ATTCGAAAAACACACCCACTACTAAAAATTATCAACCACT",
file = "dna2.fas", sep = "\n")
cat(
">No305",
"NTTCGAAAAACACACCCACTACTAAAANTTATCAGTCACT",
file = "dna3.fas", sep = "\n")

raw2Fas(getwd(), appendix = ".fas")

unlink("dna1.fas")
unlink("dna2.fas")
unlink("dna3.fas")

## 1.3 importing phy, nexus, and converting to fasta objects for further analysis.[进口1.3 PHY的关系作进一步的分析，并转换成Fasta对象。]

##### read.nxs() example[＃＃＃＃read.nxs（）的例子]
data(fil.nxs)
writeLines(fil.nxs, "example.nxs")
nxs <- read.nxs("example.nxs")
as.fasta(nxs)
unlink("example.nxs")

##### read.phy() example[＃＃＃＃read.phy（）的例子]
data(fil.phy)
writeLines(fil.phy, "example.phy")
phy <- read.phy("example.phy")
as.fasta(phy)
unlink("example.phy")

## 2 Check and visualising cutting patterns of restriction enzymes on sequences.[＃2检查和可视化序列的限制性内切酶的切割方式。]

## 2.1 enzCut() example[＃2.1 enzCut（）的例子]
data(enzdata)
enznames <- c("EcoRI", "Acc65I")
data(fil.phy)
fas <- ConvFas(fil = fil.phy, type = "phy")
enzCut(DNAsq = fas[2], enznames = "AluI", enzdata = enzdata)
rm(list = ls())

### 2.2  fragdat() example[＃＃2.2 fragdat（）的例子]
data(enzdata)
data(fil.phy)
fas <- ConvFas(fil = fil.phy, type = "phy")
frag.dat(fil = fas, enznames = "EcoRI", enzdata = enzdata)

## 2.3 plotenz() example[＃2.3 plotenz（）的例子]
data(enzdata)
data(fil.phy)
fas <- ConvFas(fil = fil.phy, type = "phy")
enznames <- c("EcoRI", "Acc65I", "HinfI")

plotenz(sequences = fas, enznames = enznames,
        enzdata = enzdata, side = TRUE, type = "RFLP")
               
plotenz(sequences = fas, enznames = enznames,
        enzdata = enzdata, side = FALSE, type = "RFLP")               
                               
plotenz(sequences = fas, enznames = enznames,
        enzdata = enzdata, side = TRUE, type = "TRFLP", "T3")

### 3 Sequence selection based on given primers.[＃3序列选择的基础上给定的引物。]

### clipprobe()[＃＃clipprobe（）]
## 3.1 Specify the forward and backward primer.[＃3.1指定的正向和反向引物。]
#clip the sequence between the backword and forward primer.[夹之间的退后，正向引物序列。]
forProbe = ITS1F = 'CTTGGTCATTTAGAGGAAGTAA' # forward primer should be from the 5' to 3' end.[正向引物应该是从5到3末端。]
bacProbe = ITS4 = 'GCATATCAATAAGCGGAGGA'    # backward primer[反向引物]
#only sequence with two probes found could be clipped.[只有两个探针发现的序列可以被裁剪。]

### 3.2 reading fasta data.[＃＃3.2阅读fasta格式的数据。]
directory <- system.file("extdata", package = "seqRFLP")
path <- file.path(directory, "seqs.fasta")
fas <- read.fasta(path)

## 3.3 Clipping. Find clipped sequences, this usually takes less than 1 minunite.[＃3.3剪辑。查找裁剪序列，这通常需要小于1 minunite。]
## please wait for a moment.[＃请稍等片刻。]
clipped <- clipprobe(fas, forProbe, bacProbe, tol = 0, clipped.only = TRUE)

## 3.4 Checking the results.[3.4检查的结果。]
## There are 368 selected sequences that could be clipped.[＃368选择的序列，可以被裁剪。]
length(gnames.fas(clipped))
## ... in 393 original sequences.[＃...在393原序列。]
length(gnames.fas(fas))
## Sequences that can not be clipped.[＃序列，可以不被限幅。]
setdiff(gnames.fas(fas), gnames.fas(clipped))


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。