est_rscu {cubar}

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())

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'.

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)