getTrans(seqinr)
getTrans()所属R语言包：seqinr
Generic function to translate coding sequences into proteins
翻译成蛋白质编码序列的通用功能
译者：生物统计家园网 机器人LoveR
描述----------Description----------
This function translates nucleic acid sequences into the corresponding peptide sequence. It can translate in any of the 3 forward or three reverse sense frames. In the case of reverse sense, the reverse-complement of the sequence is taken. It can translate using the standard (universal) genetic code and also with non-standard codes. Ambiguous bases can also be handled.
这个函数转换成相应的肽序列的核酸序列。它可以在任何3向前或三个反向感帧翻译。以反向感的情况下，采取的序列的反补。它可以翻译使用标准（通用）的遗传代码，并与非的标准代码。暧昧的碱基，也可以处理。
用法----------Usage----------
getTrans(object, sens = "F", NAstring = "X", ambiguous = FALSE, ...)
## S3 method for class 'SeqAcnucWeb'
getTrans(object, sens = "F", NAstring = "X", ambiguous = FALSE, ..., frame = "auto", numcode = "auto")
## S3 method for class 'SeqFastadna'
getTrans(object, sens = "F", NAstring = "X", ambiguous = FALSE, ..., frame = 0, numcode = 1)
## S3 method for class 'SeqFrag'
getTrans(object, sens = "F", NAstring = "X", ambiguous = FALSE, ..., frame = 0, numcode = 1)
参数----------Arguments----------
参数：object
an object of the class SeqAcnucWeb or SeqFastadna, or SeqFrag or a list of these objects, or an object of class qaw created by query
对象类SeqAcnucWeb或SeqFastadna或SeqFrag的列表，这些对象或类的一个对象，qaw的query创建，
参数：numcode
The ncbi genetic code number for translation. By default the standard genetic code is used, and for sequences coming from an ACNUC server the relevant genetic code is used by default.
NCBI的遗传密码翻译。默认情况下，标准的遗传密码，并为未来从一个ACNUC的服务器的序列有关的遗传密码是默认情况下使用。
参数：NAstring
How to translate amino-acids when there are ambiguous bases in codons.
如何翻译时，有暧昧碱基，在密码子的氨基酸。
参数：ambiguous
If TRUE, ambiguous bases are taken into account so that for instance GGN is translated to Gly in the standard genetic code.
如果是TRUE，考虑暧昧碱基，例如GGN被翻译成甘氨酸在标准的遗传密码。
参数：frame
Frame(s) (0,1,2) to translate. By default the frame 0 is used.
帧（S）（0,1,2）翻译。默认情况下，框架0使用。
参数：sens
Direction for translation: F for the direct strand e and R for the reverse complementary strand.
方向为翻译：F的直链E和R的反向互补链。
参数：...
further arguments passed to or from other methods
进一步的参数传递给其他方法
Details
详细信息----------Details----------
The following genetic codes are described here. The number preceding each code corresponds to numcode.
此处所描述的遗传密码。每个代码前的数对应到numcode。
1 standard
1个标准
2 vertebrate.mitochondrial
2 vertebrate.mitochondrial
3 yeast.mitochondrial
3 yeast.mitochondrial
4 protozoan.mitochondrial+mycoplasma
4 protozoan.mitochondrial +支原体
5 invertebrate.mitochondrial
5 invertebrate.mitochondrial
6 ciliate+dasycladaceal
6纤毛虫+ dasycladaceal
9 echinoderm+flatworm.mitochondrial
9棘皮类+ flatworm.mitochondrial
10 euplotid
10 euplotid
11 bacterial+plantplastid
11细菌+ plantplastid的
12 alternativeyeast
12 alternativeyeast
13 ascidian.mitochondrial
13 ascidian.mitochondrial
14 alternativeflatworm.mitochondrial
14 alternativeflatworm.mitochondrial
15 blepharism
15 blepharism
16 chlorophycean.mitochondrial
16 chlorophycean.mitochondrial
21 trematode.mitochondrial
21 trematode.mitochondrial
22 scenedesmus.mitochondrial
22 scenedesmus.mitochondrial
23 hraustochytrium.mitochondria
23 hraustochytrium.mitochondria
值----------Value----------
For a single sequence an object of class character containing the characters of the sequence, either of length 1 when as.string is TRUE, or of the length
对于一个单一的序列类的一个对象characteras.string是TRUE，或长度包含的字符序列，无论是长度为1的
（作者）----------Author(s)----------
D. Charif and J.R. Lobry and L. Palmeira
参考文献----------References----------
参见----------See Also----------
SeqAcnucWeb, SeqFastadna, SeqFrag<br> The genetic codes are given in the object SEQINR.UTIL, a more human readable form is given by the function tablecode. Use aaa to get the three-letter code for amino-acids.
SeqAcnucWeb，SeqFastadna，SeqFrag<BR>对象SEQINR.UTIL，更人性化的功能tablecode可读的形式给出了遗传密码。使用aaa得到氨基酸的三个字母的代码。
实例----------Examples----------
#[]
# List all available methods for getTrans generic function:[列出所有可用的方法getTrans通用功能：]
#[]
methods(getTrans)
#[]
# Toy CDS example invented by Leonor Palmeira:[玩具CDS发明的莱昂诺尔帕尔梅拉的例子：]
#[]
toycds <- s2c("tctgagcaaataaatcgg")
getTrans(toycds) # should be c("S", "E", "Q", "I", "N", "R")[应该是c（“S”，“E”，“Q”，“I”，“N”，“R”）]
#[]
# Toy CDS example with ambiguous bases:[玩具的CDS的例子与暧昧碱基：]
#[]
toycds2 <- s2c("tcngarcarathaaycgn")
getTrans(toycds2) # should be c("X", "X", "X", "X", "X", "X")[应该是c（“X”，“X”，“X”，“X”，“X”，“X”）]
getTrans(toycds2, ambiguous = TRUE) # should be c("S", "E", "Q", "I", "N", "R")[应该是c（“S”，“E”，“Q”，“I”，“N”，“R”）]
getTrans(toycds2, ambiguous = TRUE, numcode = 2) # should be c("S", "E", "Q", "X", "N", "R")[应该是c（“S”，“E”，“Q”，“X”，“N”，“R”）]
#[]
# Real CDS example:[真正的CDS例如：]
#[]
realcds <- read.fasta(file = system.file("sequences/malM.fasta", package ="seqinr"))[[1]]
getTrans(realcds)
# Biologically correct, only one stop codon at the end[生物正确的，只是在最后一个终止密码子]
getTrans(realcds, frame = 3, sens = "R", numcode = 6)
# Biologically meaningless, note the in-frame stop codons[生物意义的，注意在框的终止密码子]
#[]
# Complex transsplicing operations, the correct frame and the correct [复杂的转拼操作，正确的框架和正确的]
# genetic code are automatically used for translation into protein for[遗传密码会自动翻译成蛋白]
# sequences coming from an ACNUC server:[序列来从ACNUC服务器：]
#[]
## Not run: [＃不运行：]
# Need internet connection.[需要互联网连接。]
# Translation of the following EMBL entry:[翻译以下EMBL项目：]
#[]
# FT CDS join(complement(153944..154157),complement(153727..153866),[FT CDS连接（补，补（153727 .. 153866），（153944 .. 154157）]
# FT complement(152185..153037),138523..138735,138795..138955)[FT补（152185 .. 153037），138523 .. 138735,138795 ...... 138955）]
# FT /codon_start=1[FT / codon_start = 1]
choosebank("emblTP")
query("trans", "N=AE003734.PE35")
getTrans(trans$req[[1]])
## End(Not run)[＃（不执行）]
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 2012-9-30 01:19:25
