get_cscg {cubar}

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)