dinucleotides(seqinr)
dinucleotides()所属R语言包：seqinr
Statistical over- and under- representation of dinucleotides in a
在统计过，并表示二核苷酸
译者：生物统计家园网 机器人LoveR
描述----------Description----------
These two functions compute two different types of statistics for the measure of statistical dinculeotide over- and under-representation : the rho statistic, and the z-score, each computed for all 16 dinucleotides.
这两个函数计算两个不同类型的统计信息，统计dinculeotide过度和代表性不足：的rho沸石统计，和z每个计算的评分，对所有的16个二核苷酸的措施。
用法----------Usage----------
rho(sequence, wordsize = 2, alphabet = s2c("acgt"))
zscore(sequence, simulations = NULL, modele, exact = FALSE, alphabet = s2c("acgt"), ... )
参数----------Arguments----------
参数：sequence
a vector of single characters.
单字符的向量。
参数：wordsize
an integer giving the size of word (n-mer) to consider.
一个整数，字的大小（N-mer）的考虑。
参数：simulations
If NULL, analytical solution is computed when available (models base and codon). Otherwise, it should be the number of permutations for the z-score computation
NULL如果，解析解计算时（型号base和codon）。否则，它应该是在z-得分计算的排列数
参数：modele
A string of characters describing the model chosen for the random generation
选择随机生成的字符串的字符描述模型
参数：exact
Whether exact analytical calculation or an approximation should be used
无论是精确的分析计算或近似，应使用
参数：alphabet
A vector of single characters.
单个字符的矢量。
参数：...
Optional parameters for specific model permutations are passed on to permutation function.
具体型号排列的可选参数传递给permutation功能。
Details
详细信息----------Details----------
The rho statistic, as presented in Karlin S., Cardon LR. (1994), can be computed on each of the 16 dinucleotides. It is the frequence of dinucleotide xy divided by the product of frequencies of nucleotide x and nucleotide y. It is equal to 1.00 when dinucleotide xy is formed by pure chance, and it is superior (respectively inferior) to 1.00 when dinucleotide xy is over- (respectively under-) represented.
rho统计，卡林S.，差速器LR。 （1994年），可以计算每一个的16个二核苷酸。它是频率核苷酸x和核苷酸Ŷ频率的乘积除以二核苷酸的xy。等于1.00时，形成二核苷酸的xy由纯净的机会，并且当二核苷酸的xy是过度（分别根据）表示，它是优越的（分别为劣）为1.00。
The zscore statistic, as presented in Palmeira, L., Gu茅guen, L. and Lobry JR. (2006). The statistic is the normalization of the rho statistic by its expectation and variance according to a given random sequence generation model, and follows the standard normal distribution. This statistic can be computed with several models (cf. permutation for the description of each of the models). We provide analytical calculus for two of them: the base permutations model and the codon permutations model.
zscore统计，作为呈现在帕尔米拉，L.，Guéguen，L.和Lobry JR。 （2006年）。统计信息是rho的期望和方差，根据一个给定的随机序列生成模型统计的标准化，并遵循标准正态分布。这一统计数字可以计算出几种模式（参见permutation每一个模型的描述）。我们分析他们两个人的小算盘：base排列模型和codon排列模型。
The base model allows for random sequence generation by shuffling (with/without replacement) of all bases in the sequence. Analytical computations are available for this model: either as an approximation for large sequences (cf. Palmeira, L., Gu茅guen, L. and Lobry JR. (2006)), either as the exact analytical formulae (cf. Schbath, S. (1995)).
base模型允许洗牌（有/无更换）的所有序列中的碱基的随机序列生成。此模型可用于分析计算：无论是作为一个近似值大序列（参见帕尔梅拉，L.，Guéguen，L.和Lobry JR。（2006）），无论是作为精确的解析公式（参见Schbath，S.（ 1995））。
The position model allows for random sequence generation by shuffling (with/without replacement) of bases within their position in the codon (bases in position I, II or III stay in position I, II or III in the new sequence.
position模型允许随机序列生成洗牌（有/无替代他们的位置在碱基内的密码子（I，II或III留在位置碱基）I，II或III在新的序列。
The codon model allows for random sequence generation by shuffling (with/without replacement) of codons. Analytical computation is available for this model (Gautier, C., Gouy, M. and Louail, S. (1985)).
codon模型允许洗牌（有/无更换随机序列生成）的密码子。解析计算是可对该模型（戈蒂埃C.，古埃，M.和Louail等，S.（1985））。
The syncodon model allows for random sequence generation by shuffling (with/without replacement) of synonymous codons.
syncodon模型允许洗牌（有/无更换）同义密码子的随机序列生成。
值----------Value----------
a table containing the computed statistic for each dinucleotide
统计每个核苷酸包含计算表
（作者）----------Author(s)----------
Leonor Palmeira and J.R. Lobry with suggestions from Avril Coghlan.
参考文献----------References----------
for nucleic acid sequence study. Biochimie, 67:449-453.
Annu Rev Microbiol, 48:619-654.
mot dans une cha卯ne de Markov et application 脿 la recherche de mots de fr茅quence exceptionnelle dans les s茅quences d'ADN. Th猫se de l'Universit茅 Ren茅 Descartes, Paris V
are not depleted in light-exposed Prokaryotic genomes. Molecular Biology and Evolution, 23:2214-2219. http://mbe.oxfordjournals.org/cgi/reprint/23/11/2214
参见----------See Also----------
permutation
permutation
实例----------Examples----------
sequence <- sample(x = s2c("acgt"), size = 6000, replace = TRUE)
rho(sequence)
zscore(sequence, modele = "base")
zscore(sequence, modele = "base", exact = TRUE)
zscore(sequence, modele = "codon")
zscore(sequence, simulations = 1000, modele = "syncodon")
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。
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发表于 2012-9-30 01:16:27
