get_cscg: Mean Codon Stabilization Coefficients

In cubar: Codon Usage Bias Analysis

Mean Codon Stabilization Coefficients

Description

get_cscg calculates Mean Codon Stabilization Coefficients of each CDS.

Usage

get_cscg(cf, csc)

Arguments

cf	matrix of codon frequencies as calculated by count_codons().
csc	table of Codon Stabilization Coefficients as calculated by est_csc().

Value

a named vector of cscg values.

References

Presnyak V, Alhusaini N, Chen YH, Martin S, Morris N, Kline N, Olson S, Weinberg D, Baker KE, Graveley BR, et al. 2015. Codon optimality is a major determinant of mRNA stability. Cell 160:1111-1124.

Examples

# estimate CSCg of yeast genes
yeast_csc <- est_csc(yeast_cds, yeast_half_life)
cf_all <- count_codons(yeast_cds)
cscg <- get_cscg(cf_all, csc = yeast_csc)
head(cscg)
hist(cscg)

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