get_cai {cubar} | R Documentation |
Calculate CAI
Description
get_cai
calculates Codon Adaptation Index (CAI) of each input CDS
Usage
get_cai(cf, rscu)
Arguments
cf |
matrix of codon frequencies as calculated by 'count_codons()'. |
rscu |
rscu table containing CAI weight for each codon. This table could be generated with 'est_rscu' or prepared manually. |
Value
a named vector of CAI values
References
Sharp PM, Li WH. 1987. The codon Adaptation Index–a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res 15:1281-1295.
Examples
# estimate CAI of yeast genes based on RSCU of highly expressed genes
heg <- head(yeast_exp[order(-yeast_exp$fpkm), ], n = 500)
cf_all <- count_codons(yeast_cds)
cf_heg <- cf_all[heg$gene_id, ]
rscu_heg <- est_rscu(cf_heg)
cai <- get_cai(cf_all, rscu_heg)
head(cai)
hist(cai)
[Package cubar version 0.6.0 Index]