R: Codon usage

aminoacyl {ade4} | R Documentation

## Codon usage

### Description

`aminoacyl` is a list containing the codon counts of 36 genes encoding yeast aminoacyl-tRNA-synthetase(S.Cerevisiae).

### Usage

    data(aminoacyl)

### Format

`aminoacyl` is a list containing the 5 following objects:

genes

  is a vector giving the gene names.

localisation

  is a vector giving the cellular localisation of the proteins (M = mitochondrial, C = cytoplasmic, I = indetermined, CI = cyto and mito).

codon

  is a vector containing the 64 triplets.

AA

  is a factor giving the amino acid names for each codon.

usage.codon

  is a dataframe containing the codon counts for each gene.

### Source

Data prepared by D. Charif Delphine.Charif@versailles.inra.fr starting from:
http://www.expasy.org/sprot/

### References

Chiapello H., Olivier E., Landes-Devauchelle C., Nitschké P. and Risler J.L (1999) Codon usage as a tool to predict the cellular localisation of eukariotic ribosomal proteins and aminoacyl-tRNA synthetases. Nucleic Acids Res., 27, 14, 2848–2851.

### Examples

    data(aminoacyl)
    aminoacyl$genes
    aminoacyl$usage.codon
    dudi.coa(aminoacyl$usage.codon, scannf = FALSE)

[Package ade4 version 1.7-18 Index]