est_rscu | R Documentation |
est_rscu
calculates the Relative Synonymous Codon Usage (RSCU) values
for codons, which quantify the bias in synonymous codon usage. RSCU values
indicate whether a codon is used more (>1) or less (<1) frequently than
expected under uniform usage within its synonymous group.
est_rscu(
cf,
weight = 1,
pseudo_cnt = 1,
codon_table = get_codon_table(),
level = "subfam",
incl_stop = FALSE
)
cf |
A matrix of codon frequencies as calculated by |
weight |
A numeric vector of the same length as the number of sequences
in |
pseudo_cnt |
Numeric pseudo count added to avoid division by zero when few sequences are available for RSCU calculation (default: 1). |
codon_table |
A codon table defining the genetic code, derived from
|
level |
Character string specifying the analysis level: "subfam" (default, analyzes codon subfamilies) or "amino_acid" (analyzes at amino acid level). |
incl_stop |
Logical. Whether to include RSCU values for stop codons in the output (default: FALSE). |
A data.table containing the codon table with additional columns for RSCU analysis: usage frequency counts (cts), frequency proportions (prop), CAI weights (w_cai), and RSCU values (rscu). The table includes amino acid codes, full amino acid names, codons, and subfamily classifications.
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.
# Calculate RSCU for all yeast genes
cf_all <- count_codons(yeast_cds)
rscu_all <- est_rscu(cf_all)
head(rscu_all)
# Calculate RSCU for highly expressed genes (top 500)
heg <- head(yeast_exp[order(-yeast_exp$fpkm), ], n = 500)
cf_heg <- count_codons(yeast_cds[heg$gene_id])
rscu_heg <- est_rscu(cf_heg)
head(rscu_heg)
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