# Compute the automorphisms between DNA's Abelian group representations

## Documentation for package ‘GenomAutomorphism’ version 1.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

aaindex2 | List of 94 Amino Acid Matrices from AAindex
aaindex3 | Statistical protein contact potentials matrices from AAindex ver.9.2
aa_mutmat | Amino acid mutation matrix
aln | Simulated 'DNAStringSet' class object
as.AutomorphismList | Methods for AutomorphismList-class Objects
as.AutomorphismList-method | Methods for AutomorphismList-class Objects
aut3D | Compute the Automorphisms of Mutational Events Between two Codon Sequences Represented in Z5^3.
autby_coef | Automorphisms between DNA Primate BRCA1 Genes Grouped by Coefficients
autm | Automorphisms between DNA Sequences from two COVID-19 genomes
autm_3d | Automorphisms between DNA Sequences from two COVID-19 genomes
autm_z125 | Automorphisms between DNA Sequences from two COVID-19 genomes
automorphismByRanges | Get the automorphisms by ranges.
automorphismByRanges-method | Get the automorphisms by ranges.
automorphisms | Compute the Automorphisms of Mutational Events Between two Codon Sequences Represented in a Given Abelian group.
automorphisms-method | Compute the Automorphisms of Mutational Events Between two Codon Sequences Represented in a Given Abelian group.
automorphism_bycoef | Autmorphism Grouping by Coefficient
automorphism_bycoef-method | Autmorphism Grouping by Coefficient
autZ125 | Compute the Automorphisms of Mutational Events Between two Codon Sequences Represented in Z125.
autZ5 | Compute the Automorphisms of Mutational Events Between two Codon Sequences Represented in Z5.
autZ64 | Compute the Automorphisms of Mutational Events Between two Codon Sequences Represented in Z64.
base2codon | Split a DNA sequence into codons
base2codon-method | Split a DNA sequence into codons
base2int | Replace bases with integers from Z4 and Z5
base2int-method | Replace bases with integers from Z4 and Z5
base_coord | Base coordinates on a given a given Abelian group representation.
base_coord-method | Base coordinates on a given a given Abelian group representation.
brca1_aln | Multiple Sequence Alignment (MSA) of Primate BRCA1 DNA repair genes.
brca1_aln2 | Multiple Sequence Alignment (MSA) of Primate BRCA1 DNA repair genes.
brca1_autm | Automorphisms between DNA Sequences from Primate BRCA1 Genes
brca1_autm2 | Automorphisms between DNA Sequences from Primate BRCA1 Genes
codon_coord | Codon coordinates on a given a given Abelian group representation.
codon_coord-method | Codon coordinates on a given a given Abelian group representation.
conserved_regions | Conserved and Non-conserved Regions from a MSA
conserved_regions-method | Conserved and Non-conserved Regions from a MSA
covid_aln | Pairwise Sequence Alignment (MSA) of COVID-19 genomes.
covid_autm | Automorphisms between DNA Sequences from two COVID-19 genomes
cyc_aln | Multiple Sequence Alignment (MSA) of Primate Somatic Cytochrome C
cyc_autm | Automorphisms between DNA Sequences from Primate Cytochrome C Genes
GenomAutomorphism | GenomAutomorphism: An R package to compute the automorphisms between DNA sequences represented as elements from an Abelian group.
getAutomorphisms | Get Automorphisms
getAutomorphisms-method | Get Automorphisms
get_coord | DNA base/codon sequence and coordinates represented on a given Abelian group.
get_coord-method | DNA base/codon sequence and coordinates represented on a given Abelian group.
get_mutscore | Get Mutation Score from an AAindex Matrix
get_mutscore-method | Get Mutation Score from an AAindex Matrix
matrices | Get the Coordinate Representation from DNA Sequences on Specified Abelian Group
matrices-method | Get the Coordinate Representation from DNA Sequences on Specified Abelian Group
mut_type | Classification of DNA base mutations
seqranges | Get DNA sequence Ranges and Coordinates representation on a given Abelian Group
seqranges-method | Get DNA sequence Ranges and Coordinates representation on a given Abelian Group
slapply | Apply a function over a list-like object preserving its attributes
sortByChromAndEnd | Sorting 'GRanges-class' objects
sortByChromAndStart | Sorting 'GRanges-class' objects
str2chr | String to Character
str2chr-method | String to Character
str2dig | String to Digits
str2dig-method | String to Digits
translation | Translation of DNA/RNA sequences
translation-method | Translation of DNA/RNA sequences