kaks(seqinr)
kaks()所属R语言包：seqinr
Ka and Ks, also known as dn and ds, computation
嘉和Ks，也被称为dn和DS，计算
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Ks and Ka are, respectively, the number of substitutions per synonymous site and per non-synonymous site between two protein-coding genes. They are also denoted as ds and dn in the literature. The ratio of nonsynonymous (Ka) to synonymous (Ks) nucleotide substitution rates is an indicator of selective pressures on genes. A ratio significantly greater than 1 indicates positive selective pressure. A ratio around 1 indicates either neutral evolution at the protein level or an averaging of sites under positive and negative selective pressures. A ratio less than 1 indicates pressures to conserve protein sequence (i.e. purifying selection). This function estimates the Ka and Ks values for a set of aligned sequences using the method published by Li (1993) and gives the associated variance matrix.
KS和Ka分别是，每个非同义网站每个同义位点和2个蛋白质编码基因之间的替代。他们也表示在文献中为ds和dn。非同义（KA）的代名词（KS）的核苷酸替换率之比是基因选择压力的指标。 A比值显着大于1表示正的选择性压力。约1 A比值表明无论是在蛋白质水平上的中性进化或平均阳性和阴性选择压力下的站点。 A的比例小于1表示压力，节省蛋白质序列（即净化选择）。此函数估计的Ka和Ks值的一组对准的序列，使用由Li（1993）发表的方法，并给出了相关的协方差矩阵。
用法----------Usage----------
kaks(x,verbose = FALSE, debug = FALSE, forceUpperCase = TRUE)
参数----------Arguments----------
参数：x
An object of class alignment, obtained for instance by importing into R the data from an alignment file with the read.alignment function. This is typically a set of coding sequences aligned at the protein level, see reverse.align.
类的一个对象alignment，例如与read.alignment功能从线文件导入到R的数据。这通常是一个组的编码序列，在蛋白质水平对齐，请参阅reverse.align。
参数：verbose
If TRUE add to the results the value of L0, L2, L4 (respectively the number of non-synonymous sites, of 2-fold synonymous sites, of 4-fold synonymous sites), A0, A2, A4 (respectively the number of transitional changes at non-synonymous, 2-fold, and 4-fold synonymous sites ) and B0, B2, B4 (respectively the number of transversional changes at non-synonymous, 2-fold, and 4-fold synonymous sites).
如果为TRUE的值添加到结果的L0，L2，L4（分别非同义站点的数目的2倍的代名词网站，4倍的代名词网站），A0，A2，A4（分别多项过渡在非同义，2倍，4倍的代名词站点）和B0，B2，B4（分别颠换在非同义，2倍的变化，和4倍的代名词站点的数目）的变化。
参数：debug
If TRUE turns debug mode on.
如果是TRUE关闭调试模式。
参数：forceUpperCase
If TRUE, the default value, all character in sequences are forced to the upper case if at least one 'a', 'c', 'g', or 't' is found in the sequences. Turning it to FALSE if the sequences are already in upper case will save time.
如果是TRUE，默认值，所有的字符序列中的上部的情况下，如果被强制的至少一个一，c的，克，或t的是，在序列中找到。谈到它为FALSE，如果序列已经在大写将节省时间。
值----------Value----------
参数： ks
matrix of Ks values
KS值矩阵
参数： ka
matrix of Ka values
Ka值矩阵
参数： vks
variance matrix of Ks
Ks的方差矩阵
参数： vka
variance matrix of Ka
嘉方差矩阵
注意----------Note----------
Computing Ka and Ks makes sense for coding sequences that have been aligned at the amino-acid level before retro-translating the alignement at the nucleic acid level to ensure that sequences are compared on a codon-by-codon basis. Function reverse.align may help for this.
计算嘉和Ks有意义的编码序列已对准复古- - 翻译alignement的核酸水平上，以确保该序列之前，在氨基酸水平上的密码子密码子为基础相比。函数reverse.align可以帮助这一点。
As from seqinR 2.0-3, when there is at least one non ACGT base in a codon, this codon is considered as a gap-codon (---). This makes the computation more robust with respect to alignments with out-of-frame gaps, see example section.
作为2.0-3从seqinR，当有至少一个非ACGT碱基中的密码子，该密码子视为间隙密码子（---）。这使得计算更加强大的帧间隙路线，请参见示例部分。
Gap-codons (---) are not used for computations.
间隙的密码子（---）不用于计算。
When the alignment does not contain enough information (i.e. close to saturation), the Ka and Ks values are forced to 10.
，当对准不包含足够的信息（即接近饱和），在Ka和Ks值被强制到10。
Negative values indicate that Ka and Ks can not be computed.
负值表示不能计算，嘉和Ks。
According to Li (1993) J. Mol. Evol. 36(1):96-99, the rate of synonymous substitutions Ks is computed as: Ks = (L2.A2 + L4.A4) / (L2 + L4) + B4
据李（1993）J.摩尔。 EVOL。 36（1）:96-99，KS是计算为：KS =（L2.A2 + L4.A4）/（L2 + L4）+ B4同义替换率
and the rate of non-synonymous substitutions Ka is computed as: Ka = A0 + (L0.B0 + L2.B2) / (L0 + L2)
和非同义替换率被计算为：嘉= A0 +（L0.B0 + L2.B2）/（L0 + L2），嘉
（作者）----------Author(s)----------
D. Charif, J.R. Lobry
参考文献----------References----------
J. Mol. Evol., 36:96-99.<br>
Trends Genet., 18:486-486.<br>
needed here to trace back the original C source so as to credit correct source. The original FORTRAN-77 code by Chung-I Wu modified by Ken Wolfe is available here http://wolfe.gen.tcd.ie/lab/pub/li93/.<br>
rates of synonymous and nonsynonymous nucleotide substitutions. Mol. Biol. Evol, 21:2290-2298.<br>
at your R prompt.
参见----------See Also----------
read.alignment to import alignments from files, reverse.align to align CDS at the aa level.
read.alignment导入的路线从文件，reverse.align对齐CDS在AA级。
实例----------Examples----------
#[]
# Simple Toy example:[简单的玩具例子：]
#[]
s <- read.alignment(file = system.file("sequences/test.phylip", package = "seqinr"), format = "phylip")
kaks(s)
#[]
# Check numeric results on an simple test example:[一个简单的测试，例如检查数值结果：]
#[]
data(AnoukResult)
Anouk <- read.alignment(file = system.file("sequences/Anouk.fasta", package = "seqinr"), format = "fasta")
## if( ! all.equal(kaks(Anouk), AnoukResult) ) {[＃如果（（kaks（阿努克），AnoukResult的）！all.equal）]
## warning("Poor numeric results with respect to AnoukResult standard")[＃警告（“就AnoukResult标准差数值结果”）]
## } else {[＃} {]
## print("Results are consistent with AnoukResult standard")[＃打印（“结果符合AnoukResult标准的”）]
## }[＃}]
#[]
# As from seqinR 2.0-3 the following alignment with out-of-frame gaps[从seqinR 2.0-3以下对齐的帧间隙]
# should return a zero Ka value.[应该返回一个零的Ka值。]
#[]
# >Reference[>参考]
# ATGTGGTCGAGATATCGAAAGCTAGGGATATCGATTATATATAGCAAGATCGATAGAGGA[ATGTGGTCGAGATATCGAAAGCTAGGGATATCGATTATATATAGCAAGATCGATAGAGGA]
# TCGATGATCGATCGGGATCGACAGCTG[TCGATGATCGATCGGGATCGACAGCTG]
# >With out-of-frame gaps[随着帧的差距]
# AT-TGGTCCAGGTATCGTAAGCTAGGGATATCGATTATATATAGCAAGATCGATAGGGGA[AT-TGGTCCAGGTATCGTAAGCTAGGGATATCGATTATATATAGCAAGATCGATAGGGGA]
# TCGATGATCGATCGGGA--GACAGCTG[TCGATGATCGATCGGGA - GACAGCTG]
#[]
# This test example provided by Darren Obbard is now used as a routine check: [这个测试的例子由达伦Obbard提供的作为常规检查：]
#[]
Darren <- read.alignment(file = system.file("sequences/DarrenObbard.fasta", package = "seqinr"), format = "fasta")
stopifnot( all.equal(kaks(Darren)$ka[1], 0) )
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 01:20:11
