cubar (version 1.2.0)

codon_diff: Differential codon usage analysis

Description

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

Usage

codon_diff(seqs1, seqs2, codon_table = get_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.

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.

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)