uco(seqinr)
uco()所属R语言包：seqinr
Codon usage indices
密码子使用指数
译者：生物统计家园网 机器人LoveR
描述----------Description----------
uco calculates some codon usage indices: the codon counts eff, the relative frequencies freq or the Relative Synonymous Codon Usage rscu.
uco计算一些密码子的使用指标：的密码计算eff的相对频率freq或相对同义密码子的使用rscu。
用法----------Usage----------
uco(seq, frame = 0, index = c("eff", "freq", "rscu"), as.data.frame = FALSE,
NA.rscu = NA)
参数----------Arguments----------
参数：seq
a coding sequence as a vector of chars
作为向量的字符的编码序列
参数：frame
an integer (0, 1, 2) giving the frame of the coding sequence
一个整数（0，1，2）的编码序列的帧给予
参数：index
codon usage index choice, partial matching is allowed. eff for codon counts, freq for codon relative frequencies, and rscu the RSCU index
密码子使用的索引选择，允许部分匹配。 eff密码子计数，freq密码子的相对频率，和rscuRSCU指数
参数：as.data.frame
logical. If TRUE: all indices are returned into a data frame.
逻辑。如果TRUE：所有的指数都返回到一个数据框。
参数：NA.rscu
when an amino-acid is missing, RSCU are no more defined and repported as missing values (NA). You can force them to another value (typically 0 or 1) with this argument.
RSCU的氨基酸缺失时，没有更多的定义和repported的缺失值（NA）。您可以迫使他们与另一个值（通常为0或1）这种说法。
Details
详细信息----------Details----------
Codons with ambiguous bases are ignored.<br>
密码子与暧昧碱基的忽略。<BR>的
RSCU is a simple measure of non-uniform usage of synonymous codons in a coding sequence (Sharp et al. 1986). RSCU values are the number of times a particular codon is observed, relative to the number of times that the codon would be observed for a uniform synonymous codon usage (i.e. all the codons for a given amino-acid have the same probability). In the absence of any codon usage bias, the RSCU values would be 1.00 (this is the case for sequence cds in the exemple thereafter). A codon that is used less frequently than expected will have an RSCU value of less than 1.00 and vice versa for a codon that is used more frequently than expected.<br>
RSCU是一个简单的方法，在一个编码序列（Sharp等人，1986）的非均匀的同义密码子的使用。 RSCU值是观察到一个特定的密码子的时候，相对于将被观察为均匀的同义密码子的使用（即一个给定的氨基酸的所有密码子具有相同的概率）的密码子的数目的次数的数目。在没有任何密码子使用偏，RSCU值将是1.00（这是序列cds在其后的为例的情况下）。的密码子使用频率低于预期，将有比预期更频繁使用的密码子RSCU值小于1.00，反之亦然。<BR>
Do not use correspondence analysis on RSCU tables as this is a source of artifacts (Perriere and Thioulouse 2002, Suzuki et al. 2008). Within-aminoacid correspondence analysis is a simple way to study synonymous codon usage (Charif et al. 2005). For an introduction to correspondence analysis and within-aminoacid correspondence analysis see the chapter titled Multivariate analyses in the seqinR manual that ships with the seqinR package in the doc folder. You can also use internal correspondence analysis if you want to analyze simultaneously a row-block structure such as the within and between species variability (Lobry and Chessel 2003).<br>
不要使用RSCU表的对应分析，因为这是一个源的文物（Perriere和Thioulouse 2002年，铃木等人，2008）。内氨基酸的对应分析法是一种简单的方法来研究同义密码子的使用（谢里夫等人，2005）。对应分析和氨基酸内的对应分析的介绍，请参见章节多变量分析在seqinR手册，船舶的seqinR包中的doc文件夹。如果你想同时分析一排块的结构，如内和种间变异（2003年Lobry和Chessel），您也可以使用内部的对应分析。<BR>
If as.data.frame is FALSE, uco returns one of these:
如果as.data.frame是FALSE，uco返回下列其中一项：
eff a table of codon counts
EFF一个密码子表的计数
freq a table of codon relative frequencies
密码子的相对频率频率表
rscu a numeric vector of relative synonymous codon usage values
RSCU一个数值向量的相对同义密码子使用值
If as.data.frame is TRUE, uco returns a data frame with five columns:
如果as.data.frame是TRUE，uco返回一个数据框有五列：
aa a vector containing the name of amino-acid
氨基酸的向量，包含氨基酸的名称
codon a vector containing the corresponding codon
密码子的一个向量，包含相应的密码
eff a numeric vector of codon counts
EFF的数字向量的密码子计数
freq a numeric vector of codon relative frequencies
频率的数字密码子向量的相对频率
rscu a numeric vector of RSCU index
RSCU一个数值向量的RSCU指数
值----------Value----------
If as.data.frame is FALSE, the default, a table for eff and freq and a numeric vector for rscu. If as.data.frame is TRUE, a data frame with all indices is returned.
如果as.data.frame是FALSE，默认情况下，表eff和freq和一个数字矢量rscu。如果as.data.frame是TRUE，所有指标，则返回一个数据框。
（作者）----------Author(s)----------
D. Charif, J.R. Lobry, G. Perriere
参考文献----------References----------
analysis clearly differentiates highly and lowly expressed genes. Nucl. Acids. Res., 14:5125-5143.<br>
codon usage studies. Nucl. Acids. Res., 30:4548-4555.<br>
amino-acid usage in thermophilic bacteria. Journal of Applied Genetics, 44:235-261. http://jag.igr.poznan.pl/2003-Volume-44/2/pdf/2003_Volume_44_2-235-261.pdf.<br>
Synonymous Codon Usage Analyses with the ade4 and seqinR packages. Bioinformatics, 21:545-547. http://pbil.univ-lyon1.fr/members/lobry/repro/bioinfo04/.<br>
Comparison of Correspondence Analysis Methods for Synonymous Codon Usage in Bacteria. DNA Research, 15:357-365. http://dnaresearch.oxfordjournals.org/cgi/reprint/15/6/357.
实例----------Examples----------
## Show all possible codons:[＃显示所有可能的密码子：]
words()
## Make a coding sequence from this:[＃做的一个编码序列：]
(cds <- s2c(paste(words(), collapse = "")))
## Get codon counts:[＃获取密码子计数：]
uco(cds, index = "eff")
## Get codon relative frequencies:[＃获取密码子的相对频率：]
uco(cds, index = "freq")
## Get RSCU values:[＃RSCU值：]
uco(cds, index = "rscu")
## Show what happens with ambiguous bases:[＃显示会发生什么暧昧碱基：]
uco(s2c("aaannnttt"))
## Use a real coding sequence:[＃使用一个真正的编码序列：]
rcds <- read.fasta(file = system.file("sequences/malM.fasta", package = "seqinr"))[[1]]
uco( rcds, index = "freq")
uco( rcds, index = "eff")
uco( rcds, index = "rscu")
uco( rcds, as.data.frame = TRUE)
## Show what happens with RSCU when an amino-acid is missing:[＃显示时会发生什么RSCU氨基酸的缺失：]
ecolicgpe5 <- read.fasta(file = system.file("sequences/ecolicgpe5.fasta",package="seqinr"))[[1]]
uco(ecolicgpe5, index = "rscu")
## Force NA to zero:[＃强制NA零：]
uco(ecolicgpe5, index = "rscu", NA.rscu = 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。
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发表于 2012-9-30 01:26:17
