dinu_dist-methods: Calculating the dinucleotide usage difference between...
In SynMut: SynMut: Designing Synonymously Mutated Sequences with Different Genomic Signatures
Description
Usage
Arguments
Details
Value
Examples
Description
We use a least squares approach to estimate the dinucleotide usage
difference between DNA sequences
Usage
1
2
3
4
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
1
2
3
4
5
6
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)
SynMut documentation built on Nov. 8, 2020, 8:01 p.m.
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Description Usage Arguments Details Value Examples
Description
We use a least squares approach to estimate the dinucleotide usage difference between DNA sequences
Usage
1 2 3 4 |
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
1 2 3 4 5 6 | 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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