SynMut: Designing Synonymously Mutated Sequences with Different Genomic Signatures


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Documentation for package ‘SynMut’ version 1.10.0

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codon_dist Calculating the codon usage difference between sequences
codon_dist-method Calculating the codon usage difference between sequences
codon_mimic Mimic a target codon usage bias
codon_mimic-method Mimic a target codon usage bias
codon_random Generate random synonymous mutations
codon_random-method Generate random synonymous mutations
codon_to Maximize or minimize the usage of certain codon.
codon_to-method Maximize or minimize the usage of certain codon.
dinu_dist Calculating the dinucleotide usage difference between sequences
dinu_dist-method Calculating the dinucleotide usage difference between sequences
dinu_to Maximize or minimize the usage of certain dinucleotide.
dinu_to-method Maximize or minimize the usage of certain dinucleotide.
get_cu Get codon usage matrix
get_cu-method Get codon usage matrix
get_dna Get the DNAStringSet data
get_dna-method Get the DNAStringSet data
get_du Get dinucleotide usage matrix
get_du-method Get dinucleotide usage matrix
get_freq Get codon usage frequency of synonymous codons
get_freq-method Get codon usage frequency of synonymous codons
get_nu Get nucleotide usage matrix
get_nu-method Get nucleotide usage matrix
get_region Get the variable region
get_region-method Get the variable region
get_rscu Get Relative Synonymous Codon Usage (rscu) of synonymous codons
get_rscu-method Get Relative Synonymous Codon Usage (rscu) of synonymous codons
input_seq Import region / constructing regioned_dna object
input_seq-method Import region / constructing regioned_dna object
regioned_dna-class An S4 class to record DNA sequences and variable regions for mutations
seq_random Generate 'n' random DNA sequnces of length 'm'
seq_random-method Generate 'n' random DNA sequnces of length 'm'