codon_random-methods: Generate random synonymous mutations

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

Description

Generating random synonymous mutations (in user-defined region), with optionally keeping/not keeping the original codon usage bias.

Usage

codon_random(object, n = 1, keep = FALSE, ...)

## S4 method for signature 'regioned_dna'
codon_random(object, n, keep)

## S4 method for signature 'DNAStringSet'
codon_random(object, n, keep)

Arguments

object	A regioned_dna object.
n	Optional n parameter specifying what proportion of the codons to be mutate. Default value: 1.
keep	Logical parameter controling whether keeping the codon usage bias of the original sequence. Default value: FALSE.
...	...

Details

This method randomly sample synonymous codons for n propotion of every mutable codons in the sequences. This process will be likely to alter the codon usage bias of the original sequences. However the keep = TRUE argument help to preserve the codon usage bias. It is done via the synsequence function in seqinr package. The synsequence function essentially swaps the position of the synonymous codons without introducing new codons into the original sequences.

Value

A regioned_dna object containing the mutants; Or a DNAStringSet object if the input is a DNAStringSet object.

See Also

input_seq, dinu_to, codon_to, codon_mimic

Examples

filepath <- system.file("extdata", "example.fasta", package = "SynMut")
rgd.seq <- input_seq(filepath)
set.seed(2019)
get_cu(codon_random(rgd.seq, n = 0.5))
get_cu(codon_random(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,]   7   4   6   7   4   5   3   6   4   4   5   4   3   4  14   5   5   3
[2,]   8   4   5   5   4   1   2  11   4   2   1   2   5   2  10   4   4   2
     CAG CAT CCA CCC CCG CCT CGA CGC CGG CGT CTA CTC CTG CTT GAA GAC GAG GAT
[1,]  10   2   4   1   2   1   4   2   2   0   3   6   6   7   7   2  10   4
[2,]   5   1   1   2   1   4   3   3   4   1   4   3   5   6  10   7   6   8
     GCA GCC GCG GCT GGA GGC GGG GGT GTA GTC GTG GTT TAA TAC TAG TAT TCA TCC
[1,]   6   9   3   9   4   4   5   3   1   2   5   5   0   3   0   2   4   1
[2,]   5   4   1   6   7   2   4   2   1   4   4   6   0   1   0   0   3   4
     TCG TCT TGA TGC TGG TGT TTA TTC TTG TTT
[1,]   0   5   1   0   1   3   2   2   2   5
[2,]   3   2   1   2   4   1   3   5   1   5
     AAA AAC AAG AAT ACA ACC ACG ACT AGA AGC AGG AGT ATA ATC ATG ATT CAA CAC
[1,]   2   4  11   7   5   2   7   4   5   3   4   6   8   0  14   4   8   3
[2,]   5   2   8   7   5   0   7   6   4   6   2   1   4   6  10   1   6   2
     CAG CAT CCA CCC CCG CCT CGA CGC CGG CGT CTA CTC CTG CTT GAA GAC GAG GAT
[1,]   7   2   1   3   2   2   2   3   2   1   6   3   2   6   9   4   8   2
[2,]   3   1   2   2   2   2   2   4   1   3   1   5   2   4   7   8   9   7
     GCA GCC GCG GCT GGA GGC GGG GGT GTA GTC GTG GTT TAA TAC TAG TAT TCA TCC
[1,]   7  10   4   6   1   5   7   3   4   6   1   2   1   2   0   3   4   4
[2,]   3   4   3   6   2   5   5   3   2   3   6   4   0   0   0   1   2   1
     TCG TCT TGA TGC TGG TGT TTA TTC TTG TTT
[1,]   0   1   0   2   1   1   6   5   3   2
[2,]   3   3   1   0   4   3   6   3   4   7

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