est_csc: Estimate Codon Stabilization Coefficient

In cubar: Codon Usage Bias Analysis

Estimate Codon Stabilization Coefficient

Description

get_csc calculate codon occurrence to mRNA stability correlation coefficients (Default to Pearson's).

Usage

est_csc(
  seqs,
  half_life,
  codon_table = get_codon_table(),
  cor_method = "pearson"
)

Arguments

seqs	CDS sequences of all protein-coding genes. One for each gene.
half_life	data.frame of mRNA half life (gene_id & half_life are column names).
codon_table	a table of genetic code derived from get_codon_table or create_codon_table.
cor_method	method name passed to 'cor.test' used for calculating correlation coefficients.

Value

a data.table of codons and their CSCs. The columns include codon, codon stability coefficient, and correlation P-value.

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 yeast mRNA CSC
est_csc(yeast_cds, yeast_half_life)

cubar documentation built on Aug. 21, 2025, 5:40 p.m.