Differential codon usage analysis — codon

codon_diff takes two set of coding sequences and perform differential codon usage analysis.

Usage

codon_diff(seqs1, seqs2, codon_table = get_codon_table())

Arguments

seqs1: DNAStringSet, or an object that can be coerced to a DNAStringSet
seqs2: DNAStringSet, or an object that can be coerced to a DNAStringSet
codon_table: a table of genetic code derived from get_codon_table or create_codon_table.

Value

a data.table of the differential codon usage analysis. Global tests examine wthether a codon is used differently relative to all the other codons. Family tests examine whether a codon is used differently relative to other codons that encode the same amino acid. Subfamily tests examine whether a codon is used differently relative to other synonymous codons that share the same first two nucleotides. Odds ratio > 1 suggests a codon is used at higher frequency in seqs1 than in seqs2.

Examples

yeast_exp_sorted <- yeast_exp[order(yeast_exp$fpkm),]
seqs1 <- yeast_cds[names(yeast_cds) %in% head(yeast_exp_sorted$gene_id, 1000)]
seqs2 <- yeast_cds[names(yeast_cds) %in% tail(yeast_exp_sorted$gene_id, 1000)]
cudiff <- codon_diff(seqs1, seqs2)