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 1.0-4 Index]