codon_dist-methods: Calculating the codon usage difference between sequences

In SynMut: SynMut: Designing Synonymously Mutated Sequences with Different Genomic Signatures

Description

We use a least squares approach to estimate the codon usage difference between DNA sequences.

Usage

codon_dist(seq, ref)

## S4 method for signature 'ANY'
codon_dist(seq, ref)

Arguments

seq	the input DNA sequnece of DNAStringSet or regioned_dna class.
ref	the reference DNA sequnece of DNAStringSet or regioned_dna class.

Details

idea inspired by "Daniel Macedo de Melo Jorge, Ryan E. Mills, Adam S. Lauring, CodonShuffle: a tool for generating and analyzing synonymously mutated sequences, Virus Evolution, Volume 1, Issue 1, March 2015, vev012, https://doi.org/10.1093/ve/vev012"

Value

vector

Examples

filepath <- system.file("extdata", "example.fasta", package = "SynMut")
rgd.seq <- input_seq(filepath)
get_cu(rgd.seq)

mut.seq <- codon_random(rgd.seq)
codon_dist(mut.seq, rgd.seq)
mut.seq2 <- codon_random(rgd.seq, keep = TRUE)
codon_dist(mut.seq2, rgd.seq)

Example output

-------------------------------------------------------------------------------
For disccussion, please access to: https://github.com/Koohoko/SynMut/issues
-------------------------------------------------------------------------------
        
     AAA AAC AAG AAT ACA ACC ACG ACT AGA AGC AGG AGT ATA ATC ATG ATT CAA CAC
[1,]   5   2   8   9   5   7   2   4   7   4   4   5   5   4  14   3   5   1
[2,]   8   3   5   6   6   2   0  10   4   3   4   2   3   3  10   5   4   1
     CAG CAT CCA CCC CCG CCT CGA CGC CGG CGT CTA CTC CTG CTT GAA GAC GAG GAT
[1,]  10   4   3   2   1   2   4   1   0   1   2   7   5   9   7   2  10   4
[2,]   5   2   3   2   0   3   2   2   4   0   5   3   4   7  10   5   6  10
     GCA GCC GCG GCT GGA GGC GGG GGT GTA GTC GTG GTT TAA TAC TAG TAT TCA TCC
[1,]   8  10   0   9   5   2   7   2   2   3   5   3   0   2   0   3   3   1
[2,]   6   2   2   6   7   4   3   1   2   5   3   5   0   1   0   0   4   3
     TCG TCT TGA TGC TGG TGT TTA TTC TTG TTT
[1,]   1   4   1   0   1   3   3   3   0   4
[2,]   1   3   1   1   4   2   1   7   2   3
[1] 0.1944348 0.1884577
[1] 0 0

SynMut documentation built on Nov. 8, 2020, 8:01 p.m.