est_csc {cubar}

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

data.table of optimal codons.

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)