est_rscu: Estimate RSCU

In cubar: Codon Usage Bias Analysis

Estimate RSCU

Description

est_rscu returns the RSCU value of codons

Usage

est_rscu(
  cf,
  weight = 1,
  pseudo_cnt = 1,
  codon_table = get_codon_table(),
  level = "subfam"
)

Arguments

cf	matrix of codon frequencies as calculated by count_codons().
weight	a vector of the same length as seqs that gives different weights to CDSs when count codons. for example, it could be gene expression levels.
pseudo_cnt	pseudo count to avoid dividing by zero. This may occur when only a few sequences are available for RSCU calculation.
codon_table	a table of genetic code derived from get_codon_table or create_codon_table.
level	"subfam" (default) or "amino_acid". For which level to determine RSCU.

Value

a data.table of codon info. RSCU values are reported in the last column.

References

Sharp PM, Tuohy TM, Mosurski KR. 1986. Codon usage in yeast: cluster analysis clearly differentiates highly and lowly expressed genes. Nucleic Acids Res 14:5125-5143.

Examples

# compute RSCU of all yeast genes
cf_all <- count_codons(yeast_cds)
est_rscu(cf_all)

# compute RSCU of highly expressed (top 500) yeast genes
heg <- head(yeast_exp[order(-yeast_exp$fpkm), ], n = 500)
cf_heg <- count_codons(yeast_cds[heg$gene_id])
est_rscu(cf_heg)

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