Function reference • GenomAutomorphism

Package description

GenomAutomorphism-package GenomAutomorphism: GenomAutomorphism: An R package to compute the automorphisms between DNA sequences represented as elements from an Abelian group.

Codon and DNA Base Algebraic Representation

base_coord() seq2granges() base_seq2string_set() base_matrix(): DNA Sequences Methods

codon_coord(): Codon coordinates on a given a given Abelian group representation.

codon_matrix(): Codon Coordinate Matrix

CodonMatrix(): A Convenient Class to Store a Codon Coordinate in given Genetic Code cube.

get_coord(): DNA base/codon sequence and coordinates represented on a given Abelian group.

matrices(): Get the Coordinate Representation from DNA Sequences on Specified Abelian Group

seqranges(): Get DNA sequence Ranges and Coordinates representation on a given Abelian Group

Automorphisms

automorphisms(): Compute the Automorphisms of Mutational Events Between two Codon Sequences Represented in a Given Abelian group.

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.

autZ125(): Compute the Automorphisms of Mutational Events Between two Codon Sequences Represented in Z125.

aut3D(): Compute the Automorphisms of Mutational Events Between two Codon Sequences Represented in Z5^3.

Automorphisms methods

automorphismByRanges(): Get the automorphisms by ranges.

automorphism_bycoef(): Autmorphism Grouping by Coefficient

getAutomorphisms(): Get Automorphisms

conserved_regions(): Conserved and Non-conserved Regions from a MSA

as.AutomorphismList(): Methods for AutomorphismList-class Objects

mut_type(): Classification of DNA base mutations

Distance functions

codon_dist(): Weighted Manhattan Distance Between Codons

codon_dist_matrix(): Compute Codon Distance Matrix

aminoacid_dist(): Distance Between Aminoacids in Terms of Codon Distance

Utils

base2codon(): Split a DNA sequence into codons

base2int(): Replace bases with integers from Z4 and Z5

sortByChromAndStart() sortByChromAndEnd(): Sorting GRanges-class objects

slapply(): Apply a function over a list-like object preserving its attributes

dna_phychem(): DNA numerical matrix

aa_phychem_index() aa_mutmat() aa_index(): Amino acid mutation matrix

get_mutscore(): Get Mutation Score from an AAindex or a Mutation/Distance Matrix

str2chr(): String to Character

str2dig(): String to Digits

translation(): Translation of DNA/RNA sequences

mod(): Modulo Operation

modeq(): A Wrapper Calling Modular Linear Equation Solver (MLE)

modlineq(): Modular System of Linear Equation Solver (MLE)

peptide_phychem_index(): Amino acid numerical matrix

Data sets

aln: Simulated DNAStringSet class object

autm: Automorphisms between DNA Sequences from two COVID-19 genomes

cyc_aln: Multiple Sequence Alignment (MSA) of Primate Somatic Cytochrome C

autm_3d: Automorphisms between DNA Sequences from two COVID-19 genomes

autm_z125: Automorphisms between DNA Sequences from two COVID-19 genomes

cyc_autm: Automorphisms between DNA Sequences from Primate Cytochrome C Genes

autby_coef: Automorphisms between DNA Primate BRCA1 Genes Grouped by Coefficients

covid_aln: Pairwise Sequence Alignment (MSA) of COVID-19 genomes.

covid_autm: Automorphisms between DNA Sequences from two COVID-19 genomes

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

aaindex1: List of 571 Amino Acid Physicochemical Indexes from AAindex Database

aaindex2: List of 94 Amino Acid Matrices from AAindex

aaindex3: Statistical protein contact potentials matrices from AAindex ver.9.2

dna_phyche: Some Physicochemical Properties of DNA bases

cdm_z64: Codon Distance Matrices for the Standard Genetic Code on Z4