dinu_dist-methods: Calculating the dinucleotide usage difference between...
In Koohoko/SynMut: SynMut: Designing Synonymously Mutated Sequences with Different Genomic Signatures
dinu_dist R Documentation
Calculating the dinucleotide usage difference between sequences
Description
We use a least squares approach to estimate the dinucleotide usage
difference between DNA sequences
Usage
dinu_dist(seq, ref)
## S4 method for signature 'ANY'
dinu_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
similar method that applied in "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)
dinu_dist(mut.seq, rgd.seq)
Koohoko/SynMut documentation built on Jan. 9, 2023, 12:11 p.m.
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| dinu_dist | R Documentation |
Calculating the dinucleotide usage difference between sequences
Description
We use a least squares approach to estimate the dinucleotide usage difference between DNA sequences
Usage
dinu_dist(seq, ref) ## S4 method for signature 'ANY' dinu_dist(seq, ref)
Arguments
seq |
the input DNA sequnece of |
ref |
the reference DNA sequnece of |
Details
similar method that applied in "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)
dinu_dist(mut.seq, rgd.seq)
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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