R语言 seqinr包 EXP()函数中文帮助文档(中英文对照)

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EXP(seqinr)
EXP()所属R语言包：seqinr

                                        Vectors of coefficients to compute linear forms.
                                         系数向量计算线性形式。

                                         译者：生物统计家园网 机器人LoveR

描述----------Description----------

This dataset is used to compute linear forms on codon frequencies: if codfreq is a vector of codon frequencies then drop(freq %*% EXP$CG3) will return for instance the G+C content in third codon positions. Base order is the lexical order: a, c, g, t (or u).
此数据集来计算密码子频率的线性形式：codfreq是一个向量，密码子频率，然后drop(freq %*% EXP$CG3)比如返回的G+ C含量在密码子第三位置。基本顺序是词汇的顺序：A，C，G，T（或U）。


用法----------Usage----------


data(EXP)



格式----------Format----------

List of 24 vectors of coefficients
24向量系数列表




A num [1:4] 1 0 0 0
一个num [1:4] 1 0 0 0




A3 num [1:64] 1 0 0 0 1 0 0 0 1 0 ...
A3数[1:64] 1 0 0 0 1 0 0 0 1 0 ...




AGZ num [1:64] 0 0 0 0 0 0 0 0 1 0 ...
AGZ数[1:64] 0 0 0 0 0 0 0 0 1 0 ...




ARG num [1:64] 0 0 0 0 0 0 0 0 1 0 ...
ARG数[1:64] 0 0 0 0 0 0 0 0 1 0 ...




AU3 num [1:64] 1 0 0 1 1 0 0 1 1 0 ...
AU3数[1:64] 1 0 0 1 1 0 0 1 1 0 ...




BC num [1:64] 0 1 0 0 0 0 0 0 0 0 ...
公元前数[1:64] 0 1 0 0 0 0 0 0 0 0 ...




C num [1:4] 0 1 0 0
ÇNUM [1:4] 0 1 0 0




C3 num [1:64] 0 1 0 0 0 1 0 0 0 1 ...
C3数[1:64] 0 1 0 0 0 1 0 0 0 1 ...




CAI num [1:64]  0.00  0.00 -1.37 -2.98 -2.58 ...
蔡民[1:64] 0.00 0.00 -1.37 -2.98 -2.58 ...




CG num [1:4] 0 1 1 0
CG NUM [1:4] 0 1 1 0




CG1 num [1:64] 0 0 0 0 0 0 0 0 0 0 ...
CG1数[1:64] 0 0 0 0 0 0 0 0 0 0 ...




CG12 num [1:64] 0 0 0 0 0.5 0.5 0.5 0.5 0.5 0.5 ...
CG12数[1:64] 0 0 0 0 0.5 0.5 0.5 0.5 0.5 0.5 ...




CG2 num [1:64] 0 0 0 0 1 1 1 1 1 1 ...
CG2数[1:64] 0 0 0 0 1 1 1 1 1 1 ...




CG3 num [1:64] 0 1 1 0 0 1 1 0 0 1 ...
CG3数[1:64] 0 1 1 0 0 1 1 0 0 1 ...




CGN num [1:64] 0 0 0 0 0 0 0 0 0 0 ...
CGN数[1:64] 0 0 0 0 0 0 0 0 0 0 ...




F1 num [1:64]  1.026  0.239  1.026  0.239 -0.097 ...
F1数[1:64] 1.026 0.239 1.026 0.239 -0.097 ...




G num [1:4] 0 0 1 0
ĝNUM [1:4] 0 0 1 0




G3 num [1:64] 0 0 1 0 0 0 1 0 0 0 ...
G3的数量[1:64] 0 0 1 0 0 0 1 0 0 0 ...




KD num [1:64] -3.9 -3.5 -3.9 -3.5 -0.7 -0.7 -0.7 -0.7 -4.5 -0.8 ...
KD民[1:64] -3.9 -3.5 -3.9 -3.5 -0.7 -0.7 -0.7 -0.7 -4.5 -0.8 ...




Q num [1:64] 0 0 0 0 1 1 1 1 0 0 ...
Q数[1:64] 0 0 0 0 1 1 1 1 0 0 ...




QA3 num [1:64] 0 0 0 0 1 0 0 0 0 0 ...
QA3数[1:64] 0 0 0 0 1 0 0 0 0 0 ...




QC3 num [1:64] 0 0 0 0 0 1 0 0 0 0 ...
QC3数[1:64] 0 0 0 0 0 1 0 0 0 0 ...




U num [1:4] 0 0 0 1
ü民[1:4] 0 0 0 1




U3 num [1:64] 0 0 0 1 0 0 0 1 0 0 ...
U3的数量[1:64] 0 0 0 1 0 0 0 1 0 0 ...


Details

详细信息----------Details----------

It's better to work directly at the amino-acid level when computing linear forms on amino-acid frequencies so as to have a single coefficient vector. For instance EXP$KD to compute the Kyte and Doolittle hydrophaty index from codon frequencies is valid only for the standard genetic code.<br> <br> An alternative for drop(freq %*% EXP$CG3) is  sum( freq * EXP$CG3 ), but this is less efficient in terms of CPU time. The advantage of the latter, however, is that thanks to recycling rules you can use either sum( freq * EXP$A ) or sum( freq * EXP$A3 ). To do the same with the %*% operator you have to explicit the recycling rule as in  drop( freq %*% rep(EXP$A, 16)).
这是更好地直接计算线性形式时，在氨基酸水平上的氨基酸的频率，以便具有一个单一的系数向量。例如EXP$KD计算的Kyte和Doolittle hydrophaty的指数从密码子频率是仅适用于标准的遗传密码。<BR> <BR>的替代方案drop(freq %*% EXP$CG3)是 sum( freq * EXP$CG3 )，但是这是效率较低的CPU时间。后者的优点，但是，由于回收规则，您可以使用是sum( freq * EXP$A )或sum( freq * EXP$A3 )。做同样的％*％操作符，你必须明确的回收利用规则，在 drop( freq %*% rep(EXP$A, 16))。


源----------Source----------

ANALSEQ EXPFILEs for command EXP.<br> http://biomserv.univ-lyon1.fr/doclogi/docanals/manuel.html
ANALSEQ EXPFILEs命令EXP。参考http://biomserv.univ-lyon1.fr/doclogi/docanals/manuel.html


参考文献----------References----------




  
BC Good choice (Bon choix). Gouy M., Gautier C. (1982)

a measure of directionam synonymous codon usage bias, and its potential



expressivity and aromaticity are the major trends of amino-acid usage in 999 Escherichia coli chromosome-encode genes. Nucleic Acids
  
KD Kyte, J., Doolittle, R.F. (1982) A simple method for displaying the hydropathic character of a protein. J. Mol. Biol.,157


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