get_cai: Calculate CAI

In cubar: Codon Usage Bias Analysis

Calculate CAI

Description

get_cai calculates Codon Adaptation Index (CAI) of each input CDS

Usage

get_cai(cf, rscu, level = "subfam")

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.
level	"subfam" (default) or "amino_acid". For which level to determine CAI.

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)

cubar documentation built on April 3, 2025, 8:58 p.m.