EXP {seqinr}R Documentation

Vectors of coefficients to compute linear forms.

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).

Usage

data(EXP)

Format

List of 24 vectors of coefficients

A
num [1:4] 1 0 0 0
A3
num [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 ...
ARG
num [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 ...
BC
num [1:64] 0 1 0 0 0 0 0 0 0 0 ...
C
num [1:4] 0 1 0 0
C3
num [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 ...
CG
num [1:4] 0 1 1 0
CG1
num [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 ...
CG2
num [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 ...
CGN
num [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 ...
G
num [1:4] 0 0 1 0
G3
num [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 ...
Q
num [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 ...
QC3
num [1:64] 0 0 0 0 0 1 0 0 0 0 ...
U
num [1:4] 0 0 0 1
U3
num [1:64] 0 0 0 1 0 0 0 1 0 0 ...

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.

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)).

Source

ANALSEQ EXPFILEs for command EXP.
http://biomserv.univ-lyon1.fr/doclogi/docanals/manuel.html

References

citation("seqinr")

A
content in A nucleotide
A3
content in A nucleotide in third position of codon
AGZ
Arg content (aga and agg codons)
ARG
Arg content
AU3
content in A and U nucleotides in third position of codon
BC
Good choice (Bon choix). Gouy M., Gautier C. (1982) codon usage in bacteria : Correlation with gene expressivity. Nucleic Acids Research,10(22):7055-7074.
C
content in C nucleotides
C3
content in A nucleotides in third position of codon
CAI
Codon adaptation index for E. coli. Sharp, P.M., Li, W.-H. (1987) The codon adaptation index - a measure of directionam synonymous codon usage bias, and its potential applications. Nucleic Acids Research,15:1281-1295.
CG
content in G + C nucleotides
CG1
content in G + C nucleotides in first position of codon
CG12
content in G + C nucleotides in first and second position of codon
CG2
content in G + C nucleotides in second position of codon
CG3
content in G + C nucleotides in third position of codon
CGN
content in CGA + CGU + CGA + CGG
F1
From Table 2 in Lobry, J.R., Gautier, C. (1994) Hydrophobicity, expressivity and aromaticity are the major trends of amino-acid usage in 999 Escherichia coli chromosome-encode genes. Nucleic Acids Research,22:3174-3180.
G3
content in G nucleotides in third position of codon
KD
Kyte, J., Doolittle, R.F. (1982) A simple method for displaying the hydropathic character of a protein. J. Mol. Biol.,157 :105-132.
Q
content in quartet
QA3
content in quartet with the A nucleotide in third position
QC3
content in quartet with the A nucleotide in third position
U
content in U nucleotide
U3
content in U nucleotides in third position of codon

Examples

data(EXP)

[Package seqinr version 1.0-6 Index]