Compute the automorphisms between DNA's Abelian group
representations
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Documentation for package ‘GenomAutomorphism’ version 1.11.0
Help Pages
| '%%' | Modulo Operation |
| 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 |
| aa_index | Amino acid mutation matrix |
| aa_mutmat | Amino acid mutation matrix |
| aa_phychem_index | Amino acid mutation matrix |
| aln | Simulated 'DNAStringSet' class object |
| aminoacid_dist | Distance Between Aminoacids in Terms of Codon Distance |
| aminoacid_dist-method | Distance Between Aminoacids in Terms of Codon Distance |
| 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 |
| automorphism_prob | Autmorphism Probability |
| automorphism_prob-method | Autmorphism Probability |
| 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 | DNA Sequences Methods |
| base_coord-method | DNA Sequences Methods |
| base_matrix | DNA Sequences Methods |
| base_matrix-method | DNA Sequences Methods |
| base_methods | DNA Sequences Methods |
| base_seq2string_set | DNA Sequences Methods |
| base_seq2string_set-method | DNA Sequences Methods |
| 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 |
| cdm_z64 | Codon Distance Matrices for the Standard Genetic Code on Z4 |
| 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. |
| codon_dist | Weighted Manhattan Distance Between Codons |
| codon_dist-method | Weighted Manhattan Distance Between Codons |
| codon_dist_matrix | Compute Codon Distance Matrix |
| codon_matrix | Codon Coordinate Matrix |
| codon_matrix-method | Codon Coordinate Matrix |
| 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 |
| dna_phyche | Some Physicochemical Properties of DNA bases |
| dna_phychem | DNA numerical matrix |
| dna_phychem-method | DNA numerical matrix |
| 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 or a Mutation/Distance Matrix |
| get_mutscore-method | Get Mutation Score from an AAindex or a Mutation/Distance 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 |
| mod | Modulo Operation |
| mod-method | Modulo Operation |
| modlineq | Modular System of Linear Equation Solver (MLE) |
| modulo | Modulo Operation |
| mut_type | Classification of DNA base mutations |
| peptide_phychem_index | Amino acid numerical matrix |
| peptide_phychem_index-method | Amino acid numerical matrix |
| seq2granges | DNA Sequences Methods |
| seq2granges-method | DNA Sequences Methods |
| 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 |