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Mean Codon Stabilization Coefficients

Source: R/gene_index.R
get_cscg.Rd

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)
#>     YPL071C     YLL050C     YMR172W     YOR185C     YLL032C     YBR225W 
#> -0.03363596  0.07754667 -0.01943528  0.02885805 -0.01350414 -0.01366274 
hist(cscg)