Package 'GenomAutomorphism'

Amino acid mutation matrix

Description

The aminoacid similarity matrices from Amino Acid Index Database https://www.genome.jp/aaindex/ are provided here. AAindex (ver.9.2) is a database of numerical indices representing various physicochemical and biochemical properties of amino acids and pairs of amino acids.

The similarity of amino acids can be represented numerically, expressed in terms of observed mutation rate or physicochemical properties. A similarity matrix, also called a mutation matrix, is a set of 210 numerical values, 20 diagonal and 20x19/2 off-diagonal elements, used for sequence alignments and similarity searches.

Function aa_phychem_index is wrapper function to call two other functions: aa_mutmat and aa_index

Usage

aa_phychem_index(acc = NA, aaindex = NA, acc_list = FALSE, info = FALSE)

aa_mutmat(acc = NA, aaindex = c("aaindex2", "aaindex3"), acc_list = FALSE)

aa_index(acc = NA, acc_list = FALSE, info = FALSE)

Arguments

acc	Accession id for a specified mutation or contact potential matrix.
aaindex	Database where the requested accession id is locate. The possible values are: "aaindex2" or "aaindex3".
acc_list	Logical. If TRUE, then the list of available matrices ids and index names is returned.
info	Logical. if TRUE, then whole information for the physicochemical index will be returned.

Value

Depending on the user specifications, a mutation or contact potential matrix, a list of available matrices (indices) ids or index names can be returned. More specifically:

aa_mutmat:

Returns an aminoacid mutation matrix or a statistical protein contact potentials matrix.

aa_index:

Returns the specified aminoacid physicochemical indices.

Author(s)

Robersy Sanchez https://genomaths.com

See Also

aaindex1, aaindex2, aaindex3, and get_mutscore.

Examples

## Load the mutation matrices from database from the packages
data("aaindex1","aaindex2", package = "GenomAutomorphism" )

## Get the available mutation matrices
mat <- aa_mutmat(aaindex = "aaindex2", acc_list = TRUE)
mat[seq(10)]

## Return the 'Base-substitution-protein-stability matrix 
## (Miyazawa-Jernigan, 1993)'
aa_mutmat(acc = "MIYS930101", aaindex = "aaindex2")

## Return the 'BLOSUM80 substitution matrix (Henikoff-Henikoff, 1992)'
aa_mutmat(acc = "HENS920103", aaindex = "aaindex2")

## Using wrapping function
aa_phychem_index(acc = "EISD840101", aaindex = "aaindex1")

## Just the info. The information provided after the reference
## corresponds to the correlaiton of 'EISD840101' with other indices.
aa_phychem_index(acc = "EISD840101", aaindex = "aaindex1", info = TRUE)

---

List of 571 Amino Acid Physicochemical Indexes from AAindex Database

Description

The aminoacid indexes from Amino Acid Index Database https://www.genome.jp/aaindex/ are provided here. AAindex (ver.9.2) is a database of numerical indices representing various physicochemical and biochemical properties of amino acids and pairs of amino acids.

Usage

data("aaindex1", package = "GenomAutomorphism")

Format

A list carrying the the description 566 Amino Acid Indices in AAindex ver.9.2 and the text file with the matrices imported from https://www.genome.jp/aaindex/.

Author(s)

Robersy Sanchez https://genomaths.com

See Also

aaindex2 and aaindex3.

Examples

## Load the mutation matrices from database from the packages
data("aaindex1", package = "GenomAutomorphism", envir = environment())

## Get the available aminoacid indices.
mat <- aa_phychem_index(aaindex = "aaindex1", acc_list = TRUE)
mat[1:10]

---

List of 94 Amino Acid Matrices from AAindex

Description

The aminoacid similarity matrices from Amino Acid Index Database https://www.genome.jp/aaindex/ are provided here. AAindex (ver.9.2) is a database of numerical indices representing various physicochemical and biochemical properties of amino acids and pairs of amino acids.

Usage

data("aaindex2", package = "GenomAutomorphism")

Format

A list carrying the description of 94 Amino Acid Matrices in AAindex ver.9.2 and the text file of matrices imported from https://www.genome.jp/aaindex/.

Details

The similarity of amino acids can be represented numerically, expressed in terms of observed mutation rate or physicochemical properties. A similarity matrix, also called a mutation matrix, is a set of 210 numerical values, 20 diagonal and 20x19/2 off-diagonal elements, used for sequence alignments and similarity searches.

Author(s)

Robersy Sanchez https://genomaths.com

See Also

aaindex2 and aa_mutmat, and get_mutscore.

Examples

## Load the mutation matrices from database from the packages
data("aaindex2", package = "GenomAutomorphism")

## Get the available matrices
mat <- aa_mutmat(aaindex = "aaindex2", acc_list = TRUE)
mat[1:10]

---

Statistical protein contact potentials matrices from AAindex ver.9.2

Description

A statistical potential (also knowledge-based potential, empirical potential, or residue contact potential) is an energy function derived from an analysis of known structures in the Protein Data Bank.

Usage

data("aaindex3", package = "GenomAutomorphism")

Format

A list carrying the the description 47 Amino Acid Matrices in AAindex ver.9.2 and the text file of matrices imported from https://www.genome.jp/aaindex/.

Details

A list of 47 amino acid matrices from Amino Acid Index Database https://www.genome.jp/aaindex/ are provided here. AAindex is a database of numerical indices representing various physicochemical and biochemical properties of amino acids and pairs of amino acids.

The contact potential matrix of amino acids is a set of 210 numerical values, 20 diagonal and 20x19/2 off-diagonal elements, used for sequence alignments and similarity searches.

Author(s)

Robersy Sanchez https://genomaths.com

See Also

aaindex1, aaindex2, and get_mutscore.

Examples

## Load the mutation matrices from database from the packages
data("aaindex3", package = "GenomAutomorphism")

## Get the available mutation matrices
mat <- aa_mutmat(aaindex = "aaindex3", acc_list = TRUE)
mat[1:10]

---

Simulated DNAStringSet class object

Description

This is a DNAStringSet carrying a small pairwise DNA sequence alignment to be used in the examples provided for the package functions.

Usage

data("aln", package = "GenomAutomorphism")

Format

DNAStringSet class object.

Examples

data("aln", package = "GenomAutomorphism")
aln

---

Distance Between Aminoacids in Terms of Codon Distance

Description

This function computes the distance between aminoacids in terms of a statistic of the corresponding codons. The possible statistics are: 'mean', 'median', or some user defined function.

Usage

aminoacid_dist(aa1, aa2, ...)

## S4 method for signature 'character,character'
aminoacid_dist(
  aa1,
  aa2,
  weight = NULL,
  stat = c("mean", "median", "user_def"),
  genetic_code = "1",
  group = c("Z4", "Z5"),
  cube = c("ACGT", "AGCT", "TCGA", "TGCA", "CATG", "GTAC", "CTAG", "GATC", "ACTG",
    "ATCG", "GTCA", "GCTA", "CAGT", "TAGC", "TGAC", "CGAT", "AGTC", "ATGC", "CGTA",
    "CTGA", "GACT", "GCAT", "TACG", "TCAG"),
  num.cores = 1L,
  tasks = 0L,
  verbose = FALSE
)

## S4 method for signature 'DNAStringSet,ANY'
aminoacid_dist(
  aa1,
  weight = NULL,
  stat = c("mean", "median", "user_def"),
  group = c("Z4", "Z5"),
  cube = c("ACGT", "AGCT", "TCGA", "TGCA", "CATG", "GTAC", "CTAG", "GATC", "ACTG",
    "ATCG", "GTCA", "GCTA", "CAGT", "TAGC", "TGAC", "CGAT", "AGTC", "ATGC", "CGTA",
    "CTGA", "GACT", "GCAT", "TACG", "TCAG"),
  num.cores = 1L,
  tasks = 0L,
  verbose = FALSE
)

## S4 method for signature 'AAStringSet,ANY'
aminoacid_dist(
  aa1,
  weight = NULL,
  stat = c("mean", "median", "user_def"),
  group = c("Z4", "Z5"),
  cube = c("ACGT", "AGCT", "TCGA", "TGCA", "CATG", "GTAC", "CTAG", "GATC", "ACTG",
    "ATCG", "GTCA", "GCTA", "CAGT", "TAGC", "TGAC", "CGAT", "AGTC", "ATGC", "CGTA",
    "CTGA", "GACT", "GCAT", "TACG", "TCAG"),
  num.cores = 1L,
  tasks = 0L,
  verbose = FALSE
)

## S4 method for signature 'CodonGroup_OR_Automorphisms,ANY'
aminoacid_dist(
  aa1,
  weight = NULL,
  stat = c("mean", "median", "user_def"),
  group = c("Z4", "Z5"),
  cube = c("ACGT", "AGCT", "TCGA", "TGCA", "CATG", "GTAC", "CTAG", "GATC", "ACTG",
    "ATCG", "GTCA", "GCTA", "CAGT", "TAGC", "TGAC", "CGAT", "AGTC", "ATGC", "CGTA",
    "CTGA", "GACT", "GCAT", "TACG", "TCAG"),
  num.cores = 1L,
  tasks = 0L,
  verbose = FALSE
)

Arguments

aa1, aa2	A character string of codon sequences, i.e., sequences of DNA base-triplets. If only 'x' argument is given, then it must be a DNAStringSet-class object.
...	Not in use yet.
weight	A numerical vector of weights to compute weighted Manhattan distance between codons. If $weight = NULL$, then $weight = (1/4,1,1/16)$ for $group = "Z4"$ and $weight = (1/5,1,1/25)$ for $group = "Z5"$ (see codon_dist).
stat	The name of some statistical function summarizing data like 'mean', 'median', or some user defined function ('user_def'). If $stat = 'user_def'$, then function must have a logical argument named 'na.rm' addressed to remove missing (NA) data (see e.g., mean).
genetic_code	A single string that uniquely identifies the genetic code to extract. Should be one of the values in the id or name2 columns of GENETIC_CODE_TABLE.
group	A character string denoting the group representation for the given codon sequence as shown in reference (2-3).
cube	A character string denoting one of the 24 Genetic-code cubes, as given in references (2-3).
num.cores, tasks	Parameters for parallel computation using package BiocParallel-package: the number of cores to use, i.e. at most how many child processes will be run simultaneously (see bplapply and the number of tasks per job (only for Linux OS).
verbose	If TRUE, prints the progress bar.

Details

Only aminoacids sequences given in the following alphabet are accepted: "A","R","N","D","C","Q","E","G","H","I","L","K", "M","F","P", "S","T","W","Y","V", "", "-", and "X"; where symbols "" and "-" denote the presence a stop codon and of a gap, respectively, and letter "X" missing information, which are then taken as a gap.

The distance between any aminoacid and any of the non-aminoacid symbols is the ceiling of the greater distance found in the corresponding aminoacid distance matrix.

Value

A numerical vector with the pairwise distances between codons in sequences 'x' and 'y'.

References

1. Sanchez R. Evolutionary Analysis of DNA-Protein-Coding Regions Based on a Genetic Code Cube Metric. Curr. Top. Med. Chem. 2014;14: 407–417. https://doi.org/10.2174/1568026613666131204110022.

2. M. V Jose, E.R. Morgado, R. Sanchez, T. Govezensky, The 24 possible algebraic representations of the standard genetic code in six or in three dimensions, Adv. Stud. Biol. 4 (2012) 119-152.PDF.

3. R. Sanchez. Symmetric Group of the Genetic-Code Cubes. Effect of the Genetic-Code Architecture on the Evolutionary Process MATCH Commun. Math. Comput. Chem. 79 (2018) 527-560. PDF.

See Also

automorphisms and codon_coord

codon_dist

Examples

## Write down to aminoacid sequences
x <- "A*LTHMC"
y <- "AAMTDM-"

aminoacid_dist(aa1 = x, aa2 = y)

## Let's create an AAStringSet-class object
aa <- AAStringSet(c(x, y))

aminoacid_dist(aa1 = aa)

## Let's select cube "GCAT" and group "Z5"
aminoacid_dist(aa1 = aa, group = "Z5", cube = "TCGA")

---

Methods for AutomorphismList-class Objects

Description

Several methods are available to be applied on Automorphism-class and AutomorphismList-class objects.

Usage

as.AutomorphismList(x, grs = GRanges(), ...)

## S4 method for signature 'GRangesList,GRanges_OR_NULL'
as.AutomorphismList(x, grs = GRanges(), ...)

## S4 method for signature 'list,GRanges_OR_NULL'
as.AutomorphismList(x, grs = GRanges(), ...)

Arguments

x	A DataFrame or a automorphisms class object.
grs	A GRanges-class object.
...	Not in use yet.

Value

The returned an AutomorphismList-class object.

See Also

automorphism_bycoef, automorphisms

Examples

## Load a dataset
data("brca1_autm", package = "GenomAutomorphism")

## Let's transforming into a list of Automorphisms-class objects
x1 <- as.list(brca1_autm[seq(2)])

## Now, object 'x1' is transformed into a AutomorphismList-class object
as.AutomorphismList(x1)

## Alternatively, let's transform the list 'x1' into a GRangesList-class 
## object.
x1 <- GRangesList(x1)

## Next, object 'x1' is transformed into a AutomorphismList-class object
as.AutomorphismList(x1)

---

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

Description

Given two codon sequences represented in the Z5^3 Abelian group, this function computes the automorphisms describing codon mutational events.

Usage

aut3D(
  seq = NULL,
  filepath = NULL,
  cube = c("ACGT", "TGCA"),
  cube_alt = c("CATG", "GTAC"),
  field = "GF5",
  start = NA,
  end = NA,
  chr = 1L,
  strand = "+",
  genetic_code = getGeneticCode("1"),
  num.cores = multicoreWorkers(),
  tasks = 0L,
  verbose = TRUE
)

Arguments

seq	An object from a DNAStringSet or DNAMultipleAlignment class carrying the DNA pairwise alignment of two sequences. The pairwise alignment provided in argument seq or the 'fasta' file filepath must correspond to codon sequences.
filepath	A character vector containing the path to a file in fasta format to be read. This argument must be given if codon & base arguments are not provided.
cube, cube_alt	A character string denoting pairs of the 24 Genetic-code cubes, as given in references (2-3). That is, the base pairs from the given cubes must be complementary each other. Such a cube pair are call dual cubes and, as shown in reference (3), each pair integrates group.
field	A character string denoting the Galois field where the 3D automorphisms are estimated. This can be 'GF(4)' or 'GF(5)', but only 'GF(5)' is implemented so far.
start, end, chr, strand	Optional parameters required to build a GRanges-class. If not provided the default values given for the function definition will be used.
genetic_code	The named character vector returned by getGeneticCode or similar. The translation of codon into aminoacids is a valuable information useful for downstream statistical analysis. The standard genetic code is the default argument value applied in the translation of codons into aminoacids (see GENETIC_CODE_TABLE.
num.cores, tasks	Parameters for parallel computation using package BiocParallel-package: the number of cores to use, i.e. at most how many child processes will be run simultaneously (see bplapply and the number of tasks per job (only for Linux OS).
verbose	If TRUE, prints the progress bar.

Details

Automorphisms in Z5^3' are described as functions $f(x) = A x mod Z5$, where A is diagonal matrix, as noticed in reference (4).

Value

An object Automorphism-class with four columns on its metacolumn named: seq1, seq2, autm, and cube.

Author(s)

Robersy Sanchez (https://genomaths.com).

References

1. Sanchez R, Morgado E, Grau R. Gene algebra from a genetic code algebraic structure. J Math Biol. 2005 Oct;51(4):431-57. doi: 10.1007/s00285-005-0332-8. Epub 2005 Jul 13. PMID: 16012800. ( PDF).

2. Robersy Sanchez, Jesus Barreto (2021) Genomic Abelian Finite Groups. https://doi.org/10.1101/2021.06.01.446543.

3. M. V Jose, E.R. Morgado, R. Sanchez, T. Govezensky, The 24 possible algebraic representations of the standard genetic code in six or in three dimensions, Adv. Stud. Biol. 4 (2012) 119-152.PDF.

4. R. Sanchez. Symmetric Group of the Genetic-Code Cubes. Effect of the Genetic-Code Architecture on the Evolutionary Process MATCH Commun. Math. Comput. Chem. 79 (2018) 527-560. PDF.

Examples

## Load a pairwise alignment
data("aln", package = "GenomAutomorphism")
aln

## Automorphism on Z5^3
autms <- aut3D(seq = aln)
autms

---

Automorphisms between DNA Primate BRCA1 Genes Grouped by Coefficients

Description

This is a AutomorphismList object carrying a list of pairwise automorphisms between the DNA sequences from the MSA of primate somatic cytochrome C grouped by automorphism's coefficients. The grouping derives from the dataset brca1_autm after applying function automorphism_bycoef.

Usage

data("autby_coef", package = "GenomAutomorphism")

Format

AutomorphismByCoefList class object.

Examples

## Load the data set
data("autby_coef", package = "GenomAutomorphism")
autby_coef

## Mutation type found in the data
unique(autby_coef$human_1.human_2$mut_type)

---

Automorphisms between DNA Sequences from two COVID-19 genomes

Description

This is a AutomorphismList object carrying a list of pairwise automorphisms between the SARS coronavirus GZ02 (GenBank: AY390556.1: 265-13398_13398-21485) and Bat SARS-like coronavirus isolate bat-SL-CoVZC45 (GenBank: MG772933.1:265-1345513455-21542), nonstructural_polyprotein. The pairwise DNA sequence alignment is available in the dataset named covid_aln and the automorphisms were estimated with function autZ64.

Usage

data("autm", package = "GenomAutomorphism")

Format

AutomorphismList class object.

Details

The alignment of these DNA sequences is available at: https://github.com/genomaths/seqalignments/raw/master/COVID-19 in the fasta file 'AY390556.1_265-13398_13398-21485_RNA-POL_SARS_COVI_GZ02.fas'

Examples

data("autm", package = "GenomAutomorphism")
autm

---

Automorphisms between DNA Sequences from two COVID-19 genomes

Description

This is a AutomorphismList object carrying a list of pairwise automorphisms between the SARS coronavirus GZ02 (GenBank: AY390556.1: 265-13398_13398-21485) and Bat SARS-like coronavirus isolate bat-SL-CoVZC45 (GenBank: MG772933.1:265-1345513455-21542), nonstructural_polyprotein. The pairwise DNA sequence alignment is available in the dataset named covid_aln and the automorphisms were estimated with function aut3D.

Usage

data("autm_3d", package = "GenomAutomorphism")

Format

AutomorphismList class object.

Examples

data("autm_3d", package = "GenomAutomorphism")
autm_3d

---

Automorphisms between DNA Sequences from two COVID-19 genomes

Description

This is a AutomorphismList object carrying a list of pairwise automorphisms between the SARS coronavirus GZ02 (GenBank: AY390556.1: 265-13398_13398-21485) and Bat SARS-like coronavirus isolate bat-SL-CoVZC45 (GenBank: MG772933.1:265-1345513455-21542), nonstructural_polyprotein. The pairwise DNA sequence alignment is available in the dataset named covid_aln and the automorphisms were estimated with function autZ125.

Usage

data("autm_z125", package = "GenomAutomorphism")

Format

AutomorphismList class object.

Examples

data("autm_z125", package = "GenomAutomorphism")
autm_z125

---

Autmorphism Grouping by Coefficient

Description

Automorphisms with the same automorphism's coefficients are grouped.

Usage

automorphism_bycoef(x, ...)

## S4 method for signature 'Automorphism'
automorphism_bycoef(x, mut.type = TRUE)

## S4 method for signature 'AutomorphismList'
automorphism_bycoef(
  x,
  min.len = 1L,
  mut.type = TRUE,
  num.cores = multicoreWorkers(),
  tasks = 0L,
  verbose = TRUE
)

Arguments

x	An automorphism-class object returned by function automorphisms.
...	Not in use.
mut.type	Logical. Whether to include the mutation type as given by function mut_type.
min.len	Minimum length of a range to be reported.
num.cores, tasks	Integers. Argument num.cores denotes the number of cores to use, i.e. at most how many child processes will be run simultaneously (see bplapply function from BiocParallel package). Argument tasks denotes the number of tasks per job. value must be a scalar integer >= 0L. In this documentation a job is defined as a single call to a function, such as bplapply. A task is the division of the $X$ argument into chunks. When tasks == 0 (default), $X$ is divided as evenly as possible over the number of workers (see MulticoreParam from BiocParallel package).
verbose	logic(1). If TRUE, enable progress bar.

Value

An AutomorphismByCoef class object. A coefficient with 0 value is assigned to mutational events that are not automorphisms, e.g., indel mutations.

See Also

automorphisms

Examples

## Load dataset
data("autm", package = "GenomAutomorphism")

automorphism_bycoef(x = autm[1:2])

---

Get the automorphisms by ranges.

Description

Automorphisms estimated on a pairwise or a MSA alignment can be grouped by ranges which inherits from GRanges-class or a GRanges-class.

Usage

automorphismByRanges(x, ...)

## S4 method for signature 'Automorphism'
automorphismByRanges(x)

## S4 method for signature 'AutomorphismList'
automorphismByRanges(
  x,
  min.len = 0L,
  num.cores = multicoreWorkers(),
  tasks = 0L,
  verbose = TRUE
)

Arguments

x	An AutomorphismList-class object returned by function automorphisms.
...	Not in use.
min.len	Minimum length of a range to be reported.
num.cores, tasks	Integers. Argument num.cores denotes the number of cores to use, i.e. at most how many child processes will be run simultaneously (see bplapply function from BiocParallel package). Argument tasks denotes the number of tasks per job. value must be a scalar integer >= 0L. In this documentation a job is defined as a single call to a function, such as bplapply. A task is the division of the $X$ argument into chunks. When tasks == 0 (default), $X$ is divided as evenly as possible over the number of workers (see MulticoreParam from BiocParallel package).
verbose	logic(1). If TRUE, enable progress bar.

Value

A GRanges-class or a GRangesList-class. Each GRanges-class object with a column named cube, which carries the type of cube automorphims.

Examples

## Load dataset
data("autm", package = "GenomAutomorphism")

automorphismByRanges(x = autm[c(1, 4)])

---

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

Description

Given two codon sequences represented in a given Abelian group, this function computes the automorphisms describing codon mutational events. Basically, this function is a wrapping to call the corresponding function for a specified Abelian group.

Usage

automorphisms(seqs = NULL, filepath = NULL, group = "Z4", ...)

## S4 method for signature 'DNAStringSet_OR_NULL'
automorphisms(
  seqs = NULL,
  filepath = NULL,
  group = c("Z5", "Z64", "Z125", "Z5^3"),
  cube = c("ACGT", "TGCA"),
  cube_alt = c("CATG", "GTAC"),
  nms = NULL,
  start = NA,
  end = NA,
  chr = 1L,
  strand = "+",
  num.cores = multicoreWorkers(),
  tasks = 0L,
  verbose = TRUE
)

Arguments

seqs	An object from a DNAStringSet or DNAMultipleAlignment class carrying the DNA pairwise alignment of two sequences. The pairwise alignment provided in argument seq or the 'fasta' file filepath must correspond to codon sequences.
filepath	A character vector containing the path to a file in fasta format to be read. This argument must be given if codon & base arguments are not provided.
group	A character string denoting the group representation for the given base or codon as shown in reference (1).
...	Not in use.
cube, cube_alt	A character string denoting pairs of the 24 Genetic-code cubes, as given in references (2-3). That is, the base pairs from the given cubes must be complementary each other. Such a cube pair are call $dual cubes$ and, as shown in reference (3), each pair integrates group.
nms	Optional. Only used if the DNA sequence alignment provided carries more than two sequences. A character string giving short names for the alignments to be compared. If not given then the automorphisms between pairwise alignment are named as: 'aln_1', 'aln_2', and so on.
start, end, chr, strand	Optional parameters required to build a GRanges-class. If not provided the default values given for the function definition will be used.
num.cores, tasks	Parameters for parallel computation using package BiocParallel-package: the number of cores to use, i.e. at most how many child processes will be run simultaneously (see bplapply and the number of tasks per job (only for Linux OS).
verbose	If TRUE, prints the progress bar.

Details

Herein, automorphisms are algebraic descriptions of mutational event observed in codon sequences represented on different Abelian groups. In particular, as described in references (3-4), for each representation of the codon set on a defined Abelian group there are 24 possible isomorphic Abelian groups. These Abelian groups can be labeled based on the DNA base-order used to generate them. The set of 24 Abelian groups can be described as a group isomorphic to the symmetric group of degree four ($S_4$, see reference (4)). Function automorphismByRanges permits the classification of the pairwise alignment of protein-coding sub-regions based on the mutational events observed on it and on the genetic-code cubes that describe them.

Automorphisms in Z5, Z64 and Z125 are described as functions $f(x) = k x mod 64$ and $f(x) = k x mod 125$, where k and x are elements from the set of integers modulo 64 or modulo 125, respectively. If an automorphisms cannot be found on any of the cubes provided in the argument $cube$, then function automorphisms will search for automorphisms in the cubes provided in the argument $cube_alt$.

Automorphisms in Z5^3' are described as functions $f(x) = Ax mod Z5$, where A is diagonal matrix.

Arguments cube and cube_alt must be pairs of' dual cubes (see section 2.4 from reference 4).

Value

This function returns a Automorphism-class object with four columns on its metacolumn named: seq1, seq2, autm, and cube.

Methods

automorphismByRanges:

This function returns a GRanges-class object. Consecutive mutational events (on the codon sequence) described by automorphisms on a same cube are grouped in a range.

automorphism_bycoef

This function returns a GRanges-class object. Consecutive mutational events (on the codon sequence) described by the same automorphisms coefficients are grouped in a range.

getAutomorphisms

This function returns an AutomorphismList-class object as a list of Automorphism-class objects, which inherits from GRanges-class objects.

conserved_regions

Returns a AutomorphismByCoef class object containing the requested regions.

Author(s)

Robersy Sanchez (https://genomaths.com).

References

1. Sanchez R, Morgado E, Grau R. Gene algebra from a genetic code algebraic structure. J Math Biol. 2005 Oct;51(4):431-57. doi: 10.1007/s00285-005-0332-8. Epub 2005 Jul 13. PMID: 16012800. ( PDF).

2. Robersy Sanchez, Jesus Barreto (2021) Genomic Abelian Finite Groups. doi:10.1101/2021.06.01.446543

3. M. V Jose, E.R. Morgado, R. Sanchez, T. Govezensky, The 24 possible algebraic representations of the standard genetic code in six or in three dimensions, Adv. Stud. Biol. 4 (2012) 110-152.PDF.

4. R. Sanchez. Symmetric Group of the Genetic-Code Cubes. Effect of the Genetic-Code Architecture on the Evolutionary Process MATCH Commun. Math. Comput. Chem. 79 (2018) 527-560. PDF

See Also

autZ64.

Examples

## Load a pairwise alignment
data("aln", package = "GenomAutomorphism")
aln

## Automorphism on "Z5^3"
autms <- automorphisms(seqs = aln, group = "Z5^3", verbose = FALSE)
autms

## Automorphism on "Z64"
autms <- automorphisms(seqs = aln, group = "Z64", verbose = FALSE)
autms

## Automorphism on "Z64" from position 1 to 33
autms <- automorphisms(
    seqs = aln,
    group = "Z64",
    start = 1,
    end = 33,
    verbose = FALSE
)
autms

---

Compute the Automorphisms of Mutational Events Between two Codon Sequences Represented in Z125.

Description

Given two codon sequences represented in the Z125 Abelian group, this function computes the automorphisms describing codon mutational events.

Usage

autZ125(
  seq = NULL,
  filepath = NULL,
  cube = c("ACGT", "TGCA"),
  cube_alt = c("CATG", "GTAC"),
  start = NA,
  end = NA,
  chr = 1L,
  strand = "+",
  genetic_code = getGeneticCode("1"),
  num.cores = multicoreWorkers() - 1,
  tasks = 0L,
  verbose = TRUE
)

Arguments

seq	An object from a DNAStringSet or DNAMultipleAlignment class carrying the DNA pairwise alignment of two sequences. The pairwise alignment provided in argument seq or the 'fasta' file filepath must correspond to codon sequences.
filepath	A character vector containing the path to a file in fasta format to be read. This argument must be given if codon & base arguments are not provided.
cube, cube_alt	A character string denoting pairs of the 24 Genetic-code cubes, as given in references (2-3). That is, the base pairs from the given cubes must be complementary each other. Such a cube pair are call dual cubes and, as shown in reference (3), each pair integrates group.
start, end, chr, strand	Optional parameters required to build a GRanges-class. If not provided the default values given for the function definition will be used.
genetic_code	The named character vector returned by getGeneticCode or similar. The translation of codon into aminoacids is a valuable information useful for downstream statistical analysis. The standard genetic code is the default argument value applied in the translation of codons into aminoacids (see GENETIC_CODE_TABLE.
num.cores, tasks	Parameters for parallel computation using package BiocParallel-package: the number of cores to use, i.e. at most how many child processes will be run simultaneously (see bplapply and the number of tasks per job (only for Linux OS).
verbose	If TRUE, prints the progress bar.

Details

Automorphisms in Z125 are described as functions $f(x) = k x mod 64$, where k and x are elements from the set of integers modulo 64. As noticed in reference (1)

Value

An object Automorphism-class with four columns on its metacolumn named: seq1, seq2, autm, and cube.

References

1. Sanchez R, Morgado E, Grau R. Gene algebra from a genetic code algebraic structure. J Math Biol. 2005 Oct;51(4):431-57. doi: 10.1007/s00285-005-0332-8. Epub 2005 Jul 13. PMID: 16012800. ( PDF).

2. Robersy Sanchez, Jesus Barreto (2021) Genomic Abelian Finite Groups. doi:10.1101/2021.06.01.446543

3. M. V Jose, E.R. Morgado, R. Sanchez, T. Govezensky, The 24 possible algebraic representations of the standard genetic code in six or in three dimensions, Adv. Stud. Biol. 4 (2012) 110-152.PDF.

4. R. Sanchez. Symmetric Group of the Genetic-Code Cubes. Effect of the Genetic-Code Architecture on the Evolutionary Process MATCH Commun. Math. Comput. Chem. 79 (2018) 527-560. PDF

Examples

## Load a pairwise alignment
data("aln", package = "GenomAutomorphism")
aln

## Automorphism on Z125
autms <- autZ125(seq = aln)
autms

---

Compute the Automorphisms of Mutational Events Between two Codon Sequences Represented in Z5.

Description

Given two codon sequences represented in the Z5 Abelian group, this function computes the automorphisms describing codon mutational events.

Usage

autZ5(
  seq = NULL,
  filepath = NULL,
  cube = c("ACGT", "TGCA"),
  cube_alt = c("CATG", "GTAC"),
  start = NA,
  end = NA,
  chr = 1L,
  strand = "+",
  num.cores = multicoreWorkers(),
  tasks = 0L,
  verbose = TRUE
)

Arguments

seq	An object from a DNAStringSet or DNAMultipleAlignment class carrying the DNA pairwise alignment of two sequences.
filepath	A character vector containing the path to a file in fasta format to be read. This argument must be given if codon & base arguments are not provided.
cube, cube_alt	A character string denoting pairs of the 24 Genetic-code cubes, as given in references (2-3). That is, the base pairs from the given cubes must be complementary each other. Such a cube pair are call dual cubes and, as shown in reference (3), each pair integrates group.
start, end, chr, strand	Optional parameters required to build a GRanges-class. If not provided the default values given for the function definition will be used.
num.cores, tasks	Parameters for parallel computation using package BiocParallel-package: the number of cores to use, i.e. at most how many child processes will be run simultaneously (see bplapply and the number of tasks per job (only for Linux OS).
verbose	If TRUE, prints the progress bar.

Details

Automorphisms in Z5 are described as functions $f(x) = k x mod 64$, where k and x are elements from the set of integers modulo 64. As noticed in reference (1). The pairwise alignment provided in argument seq or the 'fasta' file filepath must correspond to DNA base sequences.

Value

An object Automorphism-class with four columns on its metacolumn named: seq1, seq2, autm, and cube.

References

1. Sanchez R, Morgado E, Grau R. Gene algebra from a genetic code algebraic structure. J Math Biol. 2005 Oct;51(4):431-57. doi: 10.1007/s00285-005-0332-8. Epub 2005 Jul 13. PMID: 16012800. ( PDF).

2. Robersy Sanchez, Jesus Barreto (2021) Genomic Abelian Finite Groups. doi:10.1101/2021.06.01.446543

3. M. V Jose, E.R. Morgado, R. Sanchez, T. Govezensky, The 24 possible algebraic representations of the standard genetic code in six or in three dimensions, Adv. Stud. Biol. 4 (2012) 110-152.PDF.

4. R. Sanchez. Symmetric Group of the Genetic-Code Cubes. Effect of the Genetic-Code Architecture on the Evolutionary Process MATCH Commun. Math. Comput. Chem. 79 (2018) 527-560. PDF

See Also

automorphisms

Examples

## Load a pairwise alignment
data("aln", package = "GenomAutomorphism")
aln

## Automorphism on Z5
autms <- autZ5(seq = aln, verbose = FALSE)
autms

---

Compute the Automorphisms of Mutational Events Between two Codon Sequences Represented in Z64.

Description

Given two codon sequences represented in the Z64 Abelian group, this function computes the automorphisms describing codon mutational events.

Usage

autZ64(
  seq = NULL,
  filepath = NULL,
  cube = c("ACGT", "TGCA"),
  cube_alt = c("CATG", "GTAC"),
  start = NA,
  end = NA,
  chr = 1L,
  strand = "+",
  genetic_code = getGeneticCode("1"),
  num.cores = multicoreWorkers(),
  tasks = 0L,
  verbose = TRUE
)

Arguments

seq	An object from a DNAStringSet or DNAMultipleAlignment class carrying the DNA pairwise alignment of two sequences. The pairwise alignment provided in argument seq or the 'fasta' file filepath must correspond to codon sequences.
filepath	A character vector containing the path to a file in fasta format to be read. This argument must be given if codon & base arguments are not provided.
cube, cube_alt	A character string denoting pairs of the 24 Genetic-code cubes, as given in references (2-3). That is, the base pairs from the given cubes must be complementary each other. Such a cube pair are call dual cubes and, as shown in reference (3), each pair integrates group.
start, end, chr, strand	Optional parameters required to build a GRanges-class. If not provided the default values given for the function definition will be used.
genetic_code	The named character vector returned by getGeneticCode or similar. The translation of codon into aminoacids is a valuable information useful for downstream statistical analysis. The standard genetic code is the default argument value applied in the translation of codons into aminoacids (see GENETIC_CODE_TABLE.
num.cores, tasks	Parameters for parallel computation using package BiocParallel-package: the number of cores to use, i.e. at most how many child processes will be run simultaneously (see bplapply and the number of tasks per job (only for Linux OS).
verbose	If TRUE, prints the progress bar.

Details

Automorphisms in Z64 are described as functions $f(x) = k * x$ mod 64, where $k$ and $x$ are elements from the set of integers modulo 64.

Value

An object Automorphism-class with four columns on its metacolumn named: seq1, seq2, autm, and cube.

Author(s)

Robersy Sanchez (https://genomaths.com).

References

1. Sanchez R, Morgado E, Grau R. Gene algebra from a genetic code algebraic structure. J Math Biol. 2005 Oct;51(4):431-57. doi: 10.1007/s00285-005-0332-8. Epub 2005 Jul 13. PMID: 16012800. ( PDF).

2. Robersy Sanchez, Jesus Barreto (2021) Genomic Abelian Finite Groups. doi:10.1101/2021.06.01.446543

3. M. V Jose, E.R. Morgado, R. Sanchez, T. Govezensky, The 24 possible algebraic representations of the standard genetic code in six or in three dimensions, Adv. Stud. Biol. 4 (2012) 110-152.PDF.

4. R. Sanchez. Symmetric Group of the Genetic-Code Cubes. Effect of the Genetic-Code Architecture on the Evolutionary Process MATCH Commun. Math. Comput. Chem. 79 (2018) 527-560. PDF

Examples

## Load a pairwise alignment
data("aln", package = "GenomAutomorphism")
aln

## Automorphism on Z64
autms <- autZ64(seq = aln, verbose = FALSE)
autms

---

DNA Sequences Methods

Description

Base coordinates on a given Abelian group representation

Given a string denoting a codon or base from the DNA (or RNA) alphabet, function base_coord return the base coordinates in the specify genetic-code Abelian group, as given in reference (1).

DNA sequences to GRanges of bases.

Function seq2granges transform an object from DNAStringSet, DNAMultipleAlignment-class or a character into an object from BaseSeq.

BaseSeq-class object to DNAStringSet-class object.

Function base_seq2string_set transforms an object from BaseSeq into an object from DNAStringSet-class.

Usage

base_coord(base = NULL, filepath = NULL, cube = "ACGT", group = "Z4", ...)

## S4 method for signature 'DNAStringSet_OR_NULL'
base_coord(
  base = NULL,
  filepath = NULL,
  cube = c("ACGT", "AGCT", "TCGA", "TGCA", "CATG", "GTAC", "CTAG", "GATC", "ACTG",
    "ATCG", "GTCA", "GCTA", "CAGT", "TAGC", "TGAC", "CGAT", "AGTC", "ATGC", "CGTA",
    "CTGA", "GACT", "GCAT", "TACG", "TCAG"),
  group = c("Z4", "Z5"),
  start = NA,
  end = NA,
  chr = 1L,
  strand = "+"
)

seq2granges(base = NULL, filepath = NULL, ...)

## S4 method for signature 'DNAStringSet_OR_NULL'
seq2granges(
  base = NULL,
  filepath = NULL,
  start = NA,
  end = NA,
  chr = 1L,
  strand = "+",
  seq_alias = NULL,
  ...
)

base_seq2string_set(x, ...)

## S4 method for signature 'BaseSeq'
base_seq2string_set(x)

base_matrix(base, ...)

## S4 method for signature 'DNAStringSet_OR_NULL'
base_matrix(
  base,
  cube = c("ACGT", "AGCT", "TCGA", "TGCA", "CATG", "GTAC", "CTAG", "GATC", "ACTG",
    "ATCG", "GTCA", "GCTA", "CAGT", "TAGC", "TGAC", "CGAT", "AGTC", "ATGC", "CGTA",
    "CTGA", "GACT", "GCAT", "TACG", "TCAG"),
  group = c("Z4", "Z5"),
  seq_alias = NULL
)

Arguments

base	An object from a DNAStringSet or DNAMultipleAlignment class carrying the DNA pairwise alignment of two sequences.
filepath	A character vector containing the path to a file in fasta format to be read. This argument must be given if codon & base arguments are not provided.
cube	A character string denoting one of the 24 Genetic-code cubes, as given in references (2 2 3).
group	A character string denoting the group representation for the given base or codon as shown in reference (1).
...	Not in use yet.
start, end, chr, strand	Optional parameters required to build a GRanges-class. If not provided the default values given for the function definition will be used.
seq_alias	DNA sequence alias/ID and description.
x	A 'BaseSeq' class object.

Details

Function 'base_coord'

Function base_coord is defined only for pairwise aligned sequences. Symbols "-" and "N" usually found in DNA sequence alignments to denote gaps and missing/unknown bases are represented by the number: '-1' on Z4 and '0' on Z5. In Z64 the symbol 'NA' will be returned for codons including symbols "-" and "N".

Functions 'seq2granges' and 'base_seq2string_set'

For the sake of brevity the metacolumns from the object returned by function 'seq2granges' are named as 'S1', 'S2', 'S3', and so on. The original DNA sequence alias are stored in the slot named 'seq_alias'. (see examples).

Value

Depending on the function called, different object will be returned:

Function 'base_coord'

This function returns a BaseGroup object carrying the DNA sequence(s) and their respective coordinates in the requested Abelian group of base representation (one-dimension, "Z4" or "Z5"). Observe that to get coordinates in the set of of integer numbers ("Z") is also possible but they are not defined to integrate a Abelian group. These are just used for the further insertion the codon set in the 3D space (R^3).

Function 'seq2granges'

This function returns a BaseGroup object carrying the DNA sequence(s), one base per ranges. A BaseGroup class object inherits from GRanges-class.

Function 'base_seq2string_set'

This function returns a DNAStringSet-class.

A BaseGroup-class object.

Author(s)

Robersy Sanchez https://genomaths.com

References

1. Robersy Sanchez, Jesus Barreto (2021) Genomic Abelian Finite Groups. doi:10.1101/2021.06.01.446543

2. M. V Jose, E.R. Morgado, R. Sanchez, T. Govezensky, The 24 possible algebraic representations of the standard genetic code in six or in three dimensions, Adv. Stud. Biol. 4 (2012) 119-152.PDF.

3. R. Sanchez. Symmetric Group of the Genetic-Code Cubes. Effect of the Genetic-Code Architecture on the Evolutionary Process MATCH Commun. Math. Comput. Chem. 79 (2018) 527-560.

See Also

Symmetric Group of the Genetic-Code Cubes.

codon_coord and base2int.

Symmetric Group of the Genetic-Code Cubes.

base_coord and codon_coord.

Examples

## Example 1. Let's get the base coordinates for codons "ACG"
## and "TGC":
x0 <- c("ACG", "TGC")
x1 <- DNAStringSet(x0)
x1

## Get the base coordinates on cube = "ACGT" on the Abelian group = "Z4"
base_coord(x1, cube = "ACGT", group = "Z4")

## Example 2. Load a pairwise alignment
data("aln", package = "GenomAutomorphism")
aln

## DNA base representation in the Abelian group Z4
bs_cor <- base_coord(
    base = aln,
    cube = "ACGT"
)
bs_cor

## Example 3. DNA base representation in the Abelian group Z5
bs_cor <- base_coord(
    base = aln,
    cube = "ACGT",
    group = "Z5"
)
bs_cor

## Example 4. Load a multiple sequence alignment (MSA) of primate BRCA1 DNA  
## repair genes 
data("brca1_aln2", package = "GenomAutomorphism")
brca1_aln2

## Get BaseSeq-class object
gr <- seq2granges(brca1_aln2)
gr

## Transform the BaseSeq-class object into a DNAStringSet-class object
str_set <- base_seq2string_set(gr)
str_set

## Recovering the original MSA
DNAMultipleAlignment(as.character(str_set))

## Example 5. 
base_matrix(base = aln, cube = "CGTA", group = "Z5")

## Example 5.

---

Split a DNA sequence into codons

Description

This function split a DNA sequence into a codon sequence.

Usage

base2codon(x, ...)

## S4 method for signature 'character'
base2codon(x)

## S4 method for signature 'DNAStringSet'
base2codon(x)

## S4 method for signature 'DNAMultipleAlignment'
base2codon(x)

Arguments

x	A character string, DNAStringSet-class or DNAMultipleAlignment-class object carrying the a DNA sequence.
...	Not in use.

Details

It is expected that the provided DNA sequence is multiple of 3, otherwise gaps are added to the end of the sequence.

Value

If the argument of 'x' is character string, then a character vector of codons will returned. If the argument of 'x' is DNAStringSet-class or DNAMultipleAlignment-class object, then a matrix of codons is returned.

Author(s)

Robersy Sanchez https://genomaths.com. 01/15/2022

Examples

## Gaps are added at the sequence end.
seq <- c("ACCT")
base2codon(x = seq)

## This DNA sequence is multiple of 3
seq <- c("ACCTCA")
base2codon(x = seq)

## Load a DNAStringSet. A matrix of codons is returned
data("aln", package = "GenomAutomorphism")
base2codon(x = aln)

---

Replace bases with integers from Z4 and Z5

Description

A simple function to represent DNA bases as elements from the Abelian group of integers modulo 4 (Z4), 5 (Z5), or 2 (Z2).

Usage

base2int(base, ...)

## S4 method for signature 'character'
base2int(
  base,
  group = c("Z4", "Z5", "Z64", "Z125", "Z4^3", "Z5^3", "Z2"),
  cube = c("ACGT", "AGCT", "TCGA", "TGCA", "CATG", "GTAC", "CTAG", "GATC", "ACTG",
    "ATCG", "GTCA", "GCTA", "CAGT", "TAGC", "TGAC", "CGAT", "AGTC", "ATGC", "CGTA",
    "CTGA", "GACT", "GCAT", "TACG", "TCAG"),
  phychem = list(A = NULL, T = NULL, C = NULL, G = NULL, N = NULL)
)

## S4 method for signature 'data.frame'
base2int(
  base,
  group = c("Z4", "Z5", "Z64", "Z125", "Z4^3", "Z5^3", "Z2"),
  cube = c("ACGT", "AGCT", "TCGA", "TGCA", "CATG", "GTAC", "CTAG", "GATC", "ACTG",
    "ATCG", "GTCA", "GCTA", "CAGT", "TAGC", "TGAC", "CGAT", "AGTC", "ATGC", "CGTA",
    "CTGA", "GACT", "GCAT", "TACG", "TCAG"),
  phychem = list(A = NULL, T = NULL, C = NULL, G = NULL, N = NULL)
)

Arguments

base	A character vector, string , or a dataframe of letters from the DNA/RNA alphabet.
...	Not in use.
group	A character string denoting the group representation for the given base or codon as shown in reference (2-3).
cube	A character string denoting one of the 24 Genetic-code cubes, as given in references (2-3).
phychem	Optional. Eventually, it could be useful to represent DNA bases by numerical values of measured physicochemical properties. If provided, then this argument must be a named numerical list. For example, the scale values of deoxyribonucleic acids proton affinity (available at https://www.wolframalpha.com/ and in cell phone app: Wolfram Alpha): $list('A' = 0.87, 'C' = 0.88, 'T' = 0.82, 'G' = 0.89, 'N' = NA)$ where symbol 'N' provide the value for any letter out of DNA base alphabet. In this example, we could write NA or 0 (see example section).

Details

For Z2 (binary representation of DNA bases), the cube bases are represented in their order by: '00', '01', '10', and '11' (examples section).

Value

A numerical vector.

Author(s)

Robersy Sanchez https://genomaths.com

References

1. Robersy Sanchez, Jesus Barreto (2021) Genomic Abelian Finite Groups. doi: 10.1101/2021.06.01.446543

2. M. V Jose, E.R. Morgado, R. Sanchez, T. Govezensky, The 24 possible algebraic representations of the standard genetic code in six or in three dimensions, Adv. Stud. Biol. 4 (2012) 119-152.PDF.

3. R. Sanchez. Symmetric Group of the Genetic-Code Cubes. Effect of the Genetic-Code Architecture on the Evolutionary Process MATCH Commun. Math. Comput. Chem. 79 (2018) 527-560.

See Also

base_coord, codon_coord, and dna_phychem.

Examples

## A triplet with a letter not from DNA/RNA alphabet
## 'NA' is introduced by coercion!
base2int("UDG")

## The base replacement in cube "ACGT and group "Z4"
base2int("ACGT")

## The base replacement in cube "ACGT and group "Z5"
base2int("ACGT", group = "Z5")

## A vector of DNA base triplets
base2int(c("UTG", "GTA"))

##  A vector of DNA base triplets with different number of triplets.
##  Codon 'GTA' is recycled!
base2int(base = c("UTGGTA", "CGA"), group = "Z5")

## Data frames 

base2int(data.frame(x1 = c("UTG", "GTA"), x2 = c("UTG", "GTA")))


## Cube bases are represented n their order by: '00', '01', '10', and '11',
## For example for cube = "ACGT" we have mapping: A -> '00', C -> '01',
## G -> '11', and C -> '10'.

base2int("ACGT", group = "Z2", cube = "ACGT")

---

Multiple Sequence Alignment (MSA) of Primate BRCA1 DNA repair genes.

Description

This is a DNAMultipleAlignment carrying a MSA of BRCA1 DNA repair genes to be used in the examples provided for the package functions. The original file can be downloaded from GitHub at: https://bit.ly/3DimROD

Usage

data("brca1_aln", package = "GenomAutomorphism")

Format

DNAMultipleAlignment class object.

See Also

brca1_aln2, brca1_autm, and covid_aln.

Examples

data("brca1_aln", package = "GenomAutomorphism")
brca1_aln

---

Multiple Sequence Alignment (MSA) of Primate BRCA1 DNA repair genes.

Description

This is a DNAMultipleAlignment carrying a MSA of BRCA1 DNA repair genes to be used in the examples provided for the package functions. The original file can be downloaded from GitHub at: https://bit.ly/3DimROD. This data set has 41 DNA sequences and it contains the previous 20 primate variants found in 'brca1_aln' data set plus 21 single mutation variants (SMV) from the human sequence NM_007298 transcript variant 4. The location of each SMV is given in the heading from each sequence.

Usage

data("brca1_aln2", package = "GenomAutomorphism")

Format

DNAMultipleAlignment class object.

Author(s)

Robersy Sanchez https://genomaths.com

See Also

brca1_aln, brca1_autm2, cyc_aln, and covid_autm.

Examples

data("brca1_aln2", package = "GenomAutomorphism")
brca1_aln2

---

Automorphisms between DNA Sequences from Primate BRCA1 Genes

Description

This is a AutomorphismList object carrying a list of pairwise automorphisms between the DNA sequences from the MSA of primate BRCA1 DNA repair gene. The automorphisms were estimated from the brca1_aln MSA with function autZ64.

Usage

data("brca1_autm", package = "GenomAutomorphism")

Format

AutomorphismList class object.

Author(s)

Robersy Sanchez https://genomaths.com

See Also

brca1_autm2, brca1_aln, brca1_aln2, and covid_autm.

Examples

data("brca1_autm", package = "GenomAutomorphism")
brca1_autm

---

Automorphisms between DNA Sequences from Primate BRCA1 Genes

Description

This is a AutomorphismList object carrying a list of pairwise automorphisms between the DNA sequences from the MSA of primate BRCA1 DNA repair gene. The data set brca1_aln2 has 41 DNA sequences and it contains the previous 20 primate variants found in 'braca1_aln' data set plus 21 single mutation variants (SMV) from the human sequence NM_007298 transcript variant 4. The location of each SMV is given in the heading from each sequence. The automorphisms were estimated from the brca1_aln MSA with function autZ64.

Usage

data("brca1_autm2", package = "GenomAutomorphism")

Format

AutomorphismList class object.

---

Codon Distance Matrices for the Standard Genetic Code on Z4

Description

This is a list of 24 codon distance matrices created with function codon_dist_matrix in the set of 24 genetic-code cubes on Z4 (using the default weights and assuming the standard genetic code (SGC). The data set is created to speed up the computation when working with DNA sequences from superior organisms. Since distance matrices are symmetric, it is enough to provide the lower matrix. Each matrix is given as named/labeled vector (see the example).

Usage

data("cdm_z64", package = "GenomAutomorphism")

Format

A list object.

Examples

## Load the data set
data("cdm_z64", package = "GenomAutomorphism")
cdm_z64

## The lower matrix (given as vector) for cube "TCGA" (picking out the 20 
## first values). Observe that this vector is labeled. Each numerical value 
## corresponds to the distance between the codons specified by the 
## name/label on it. For example, the distance between codons TTT and TCT 
## is: 0.0625.

head(cdm_z64[[ "TCGA" ]], 20)

---

Codon coordinates on a given a given Abelian group representation.

Description

Given a string denoting a codon or base from the DNA (or RNA) alphabet and a genetic-code Abelian group as given in reference (1).

Usage

codon_coord(codon = NULL, ...)

## S4 method for signature 'BaseGroup'
codon_coord(codon, group = NULL)

## S4 method for signature 'DNAStringSet_OR_NULL'
codon_coord(
  codon = NULL,
  filepath = NULL,
  cube = c("ACGT", "AGCT", "TCGA", "TGCA", "CATG", "GTAC", "CTAG", "GATC", "ACTG",
    "ATCG", "GTCA", "GCTA", "CAGT", "TAGC", "TGAC", "CGAT", "AGTC", "ATGC", "CGTA",
    "CTGA", "GACT", "GCAT", "TACG", "TCAG"),
  group = c("Z4", "Z5", "Z64", "Z125", "Z4^3", "Z5^3"),
  start = NA,
  end = NA,
  chr = 1L,
  strand = "+"
)

## S4 method for signature 'matrix_OR_data_frame'
codon_coord(
  codon,
  cube = c("ACGT", "AGCT", "TCGA", "TGCA", "CATG", "GTAC", "CTAG", "GATC", "ACTG",
    "ATCG", "GTCA", "GCTA", "CAGT", "TAGC", "TGAC", "CGAT", "AGTC", "ATGC", "CGTA",
    "CTGA", "GACT", "GCAT", "TACG", "TCAG"),
  group = c("Z64", "Z125", "Z4^3", "Z5^3")
)

Arguments

codon	An object from BaseGroup-class (generated with function base_coord), DNAStringSet or from DNAMultipleAlignment class carrying the DNA pairwise alignment of two sequences.
...	Not in use.
group	A character string denoting the group representation for the given base or codon as shown in reference (2-3).
filepath	A character vector containing the path to a file in fasta format to be read. This argument must be given if codon & base arguments are not provided.
cube	A character string denoting one of the 24 Genetic-code cubes, as given in references (2-3).
start, end, chr, strand	Optional parameters required to build a GRanges-class. If not provided the default values given for the function definition will be used.

Details

Symbols "-" and "N" usually found in DNA sequence alignments to denote gaps and missing/unknown bases are represented by the number: '-1' on Z4 and '0' on Z5. In Z64 the symbol 'NA' will be returned for codons including symbols "-" and "N".

This function returns a GRanges-class object carrying the codon sequence(s) and their respective coordinates in the requested Abelian group or simply, when group = 'Z5^3' 3D-coordinates, which are derive from Z5 as indicated in reference (3). Notice that the coordinates can be 3D or just one-dimension ("Z64" or "Z125"). Hence, the pairwise alignment provided in argument codon must correspond to codon sequences.

Value

A CodonGroup-class object.

Author(s)

Robersy Sanchez https://genomaths.com

References

1. Robersy Sanchez, Jesus Barreto (2021) Genomic Abelian Finite Groups. doi: 10.1101/2021.06.01.446543

2. M. V Jose, E.R. Morgado, R. Sanchez, T. Govezensky, The 24 possible algebraic representations of the standard genetic code in six or in three dimensions, Adv. Stud. Biol. 4 (2012) 119-152.PDF.

3. R. Sanchez. Symmetric Group of the Genetic-Code Cubes. Effect of the Genetic-Code Architecture on the Evolutionary Process MATCH Commun. Math. Comput. Chem. 79 (2018) 527-560.

See Also

Symmetric Group of the Genetic-Code Cubes.

codon_matrix, base_coord and base2int.

Examples

## Load a pairwise alignment
data("aln", package = "GenomAutomorphism")
aln

## DNA base representation in the Abelian group Z5
bs_cor <- codon_coord(
    codon = aln,
    cube = "ACGT",
    group = "Z5"
)
bs_cor ## 3-D coordinates


## DNA base representation in the Abelian group Z64
bs_cor <- codon_coord(
    codon = aln,
    cube = "ACGT",
    group = "Z64"
)
bs_cor

## Giving a matrix of codons
codon_coord(base2codon(x = aln))

---

Weighted Manhattan Distance Between Codons

Description

This function computes the weighted Manhattan distance between codons from two sequences as given in reference (1). That is, given two codons $x$ and $y$ with coordinates on the set of integers modulo 5 ("Z5"): $x = (x_1, x_2, x_3)$ and $x = (y_1, y_2, y_3)$ (see (1)), the Weighted Manhattan distance between this two codons is defined as:

$d_w(x,y) = |x_1 - y_1|/5 + |x_2 - y_2| + |x_3 -y_3|/25$

If the codon coordinates are given on "Z4", then the Weighted Manhattan distance is define as:

$d_w(x,y) = |x_1 - y_1|/4 + |x_2 - y_2| + |x_3 -y_3|/16$

Herein, we move to the generalized version given in reference (3), for which:

$d_w(x,y) = |x_1 - y_1| w_1 + |x_2 - y_2| w_2 + |x_3 -y_3| w_3$

where we use the vector of $weight = (w_1, w_2, w_3)$.

Usage

codon_dist(x, y, ...)

## S4 method for signature 'DNAStringSet'
codon_dist(
  x,
  weight = NULL,
  group = c("Z4", "Z5"),
  cube = c("ACGT", "AGCT", "TCGA", "TGCA", "CATG", "GTAC", "CTAG", "GATC", "ACTG",
    "ATCG", "GTCA", "GCTA", "CAGT", "TAGC", "TGAC", "CGAT", "AGTC", "ATGC", "CGTA",
    "CTGA", "GACT", "GCAT", "TACG", "TCAG"),
  num.cores = 1L,
  tasks = 0L,
  verbose = FALSE
)

## S4 method for signature 'character'
codon_dist(
  x,
  y,
  weight = NULL,
  group = c("Z4", "Z5"),
  cube = c("ACGT", "AGCT", "TCGA", "TGCA", "CATG", "GTAC", "CTAG", "GATC", "ACTG",
    "ATCG", "GTCA", "GCTA", "CAGT", "TAGC", "TGAC", "CGAT", "AGTC", "ATGC", "CGTA",
    "CTGA", "GACT", "GCAT", "TACG", "TCAG"),
  num.cores = 1L,
  tasks = 0L,
  verbose = FALSE
)

## S4 method for signature 'CodonGroup_OR_Automorphisms'
codon_dist(
  x,
  weight = NULL,
  group = c("Z4", "Z5"),
  cube = c("ACGT", "AGCT", "TCGA", "TGCA", "CATG", "GTAC", "CTAG", "GATC", "ACTG",
    "ATCG", "GTCA", "GCTA", "CAGT", "TAGC", "TGAC", "CGAT", "AGTC", "ATGC", "CGTA",
    "CTGA", "GACT", "GCAT", "TACG", "TCAG"),
  num.cores = 1L,
  tasks = 0L,
  verbose = FALSE
)

Arguments

x, y	A character string of codon sequences, i.e., sequences of DNA base-triplets. If only 'x' argument is given, then it must be a DNAStringSet-class object.
...	Not in use yet.
weight	A numerical vector of weights to compute weighted Manhattan distance between codons. If $weight = NULL$, then $weight = (1/4,1,1/16)$ for $group = "Z4"$ and $weight = (1/5,1,1/25)$ for $group = "Z5"$.
group	A character string denoting the group representation for the given codon sequence as shown in reference (2-3).
cube	A character string denoting one of the 24 Genetic-code cubes, as given in references (2-3).
num.cores, tasks	Parameters for parallel computation using package BiocParallel-package: the number of cores to use, i.e. at most how many child processes will be run simultaneously (see bplapply and the number of tasks per job (only for Linux OS).
verbose	If TRUE, prints the progress bar.

Value

A numerical vector with the pairwise distances between codons in sequences 'x' and 'y'.

References

1. Sanchez R. Evolutionary Analysis of DNA-Protein-Coding Regions Based on a Genetic Code Cube Metric. Curr Top Med Chem. 2014;14: 407–417. https://doi.org/10.2174/1568026613666131204110022.

2. M. V Jose, E.R. Morgado, R. Sanchez, T. Govezensky, The 24 possible algebraic representations of the standard genetic code in six or in three dimensions, Adv. Stud. Biol. 4 (2012) 119-152.PDF.

3. R. Sanchez. Symmetric Group of the Genetic-Code Cubes. Effect of the Genetic-Code Architecture on the Evolutionary Process MATCH Commun. Math. Comput. Chem. 79 (2018) 527-560. PDF.

See Also

codon_dist_matrix, automorphisms, codon_coord, and aminoacid_dist.

Examples

## Let's write two small DNA sequences
x = "ACGCGTGTACCGTGACTG"
y = "TGCGCCCGTGACGCGTGA"

codon_dist(x, y, group = "Z5")

## Alternatively, data can be vectors of codons, i.e., vectors of DNA 
## base-triplets (including gaps simbol "-").
x = c("ACG","CGT","GTA","CCG","TGA","CTG","ACG")
y = c("TGC","GCC","CGT","GAC","---","TGA","A-G")

## Gaps are not defined on "Z4"
codon_dist(x, y, group = "Z4")

## Gaps are considered on "Z5"
codon_dist(x, y, group = "Z5")

## Load an Automorphism-class object
data("autm", package = "GenomAutomorphism")
codon_dist(x = head(autm,20), group = "Z4")

## Load a pairwise alignment
data("aln", package = "GenomAutomorphism")
aln

codon_dist(x = aln, group = "Z5")

---

Compute Codon Distance Matrix

Description

This function computes the codon distance matrix based on the weighted Manhattan distance between codons estimated with function codon_dist.

Usage

codon_dist_matrix(
  genetic_code = "1",
  group = c("Z4", "Z5"),
  weight = NULL,
  cube = c("ACGT", "AGCT", "TCGA", "TGCA", "CATG", "GTAC", "CTAG", "GATC", "ACTG",
    "ATCG", "GTCA", "GCTA", "CAGT", "TAGC", "TGAC", "CGAT", "AGTC", "ATGC", "CGTA",
    "CTGA", "GACT", "GCAT", "TACG", "TCAG"),
  output = c("list", "vector", "dist"),
  num.cores = 1L
)

Arguments

genetic_code	A single string that uniquely identifies the genetic code to extract. Should be one of the values in the id or name2 columns of GENETIC_CODE_TABLE.
group	A character string denoting the group representation for the given codon sequence as shown in reference (2-3).
weight	A numerical vector of weights to compute weighted Manhattan distance between codons. If $weight = NULL$, then $weight = (1/4,1,1/16)$ for $group =$ "Z4" and $weight = (1/5,1,1/25)$ for $group =$ "Z5" (see codon_dist).
cube	A character string denoting one of the 24 Genetic-code cubes, as given in references (2-3).
output	Format of the returned lower triangular matrix: as a list of 63 elements (labeled) or as a labeled vector using codons as labels.
num.cores	An integer to setup the number of parallel workers via makeCluster.

Details

By construction, a distance matrix is a symmetric matrix. Hence, the knowledge of lower triangular matrix is enough for its application to any downstream analysis.

Value

A lower triangular matrix excluding the diagonal.

See Also

codon_dist.

Examples

## The distance matrix for codons for the Invertebrate Mitochondrial,
## cube "TGCA" with base-triplet represented on the group "Z5". Each 
## coordinate from each returned numerical vector corresponds to the 
## distance between codons given in the coordinate name. 
x <- codon_dist_matrix(genetic_code = "5", cube = "TGCA", group = "Z5",
                    output = "vector")
x[seq(61, 63)]

---

Codon Coordinate Matrix

Description

This function build the coordinate matrix for each sequence from an aligned set of DNA codon sequences.

Usage

codon_matrix(base, ...)

## S4 method for signature 'BaseSeqMatrix'
codon_matrix(base, num.cores = 1L, tasks = 0L, verbose = TRUE, ...)

## S4 method for signature 'DNAStringSet'
codon_matrix(
  base,
  cube = c("ACGT", "AGCT", "TCGA", "TGCA", "CATG", "GTAC", "CTAG", "GATC", "ACTG",
    "ATCG", "GTCA", "GCTA", "CAGT", "TAGC", "TGAC", "CGAT", "AGTC", "ATGC", "CGTA",
    "CTGA", "GACT", "GCAT", "TACG", "TCAG"),
  group = c("Z4", "Z5"),
  num.cores = 1L,
  tasks = 0L,
  verbose = TRUE
)

## S4 method for signature 'DNAMultipleAlignment'
codon_matrix(
  base,
  cube = c("ACGT", "AGCT", "TCGA", "TGCA", "CATG", "GTAC", "CTAG", "GATC", "ACTG",
    "ATCG", "GTCA", "GCTA", "CAGT", "TAGC", "TGAC", "CGAT", "AGTC", "ATGC", "CGTA",
    "CTGA", "GACT", "GCAT", "TACG", "TCAG"),
  group = c("Z4", "Z5"),
  num.cores = 1L,
  tasks = 0L,
  verbose = TRUE
)

Arguments

base	A DNAMultipleAlignment, a DNAStringSet, or a BaseSeqMatrix.
...	Not in use yet.
num.cores, tasks	Parameters for parallel computation using package BiocParallel-package: the number of cores to use, i.e. at most how many child processes will be run simultaneously (see bplapply and the number of tasks per job (only for Linux OS).
verbose	If TRUE, prints the function log to stdout
cube	A character string denoting one of the 24 Genetic-code cubes, as given in references (3-4).
group	A character string denoting the group representation for the given base or codon as shown in reference (3-4).

Details

The purpose of this function is making the codon coordinates from multiple sequence alignments (MSA) available for further downstream statistical analyses, like those reported in references (1) and (2).

Value

A ListCodonMatrix class object with the codon coordinate on its metacolumns.

Author(s)

Robersy Sanchez https://genomaths.com

References

1. Lorenzo-Ginori, Juan V., Aníbal Rodríguez-Fuentes, Ricardo Grau Ábalo, and Robersy Sánchez Rodríguez. "Digital signal processing in the analysis of genomic sequences." Current Bioinformatics 4, no. 1 (2009): 28-40.

2. Sanchez, Robersy. "Evolutionary analysis of DNA-protein-coding regions based on a genetic code cube metric." Current Topics in Medicinal Chemistry 14, no. 3 (2014): 407-417.

3. Robersy Sanchez, Jesus Barreto (2021) Genomic Abelian Finite Groups. doi: 10.1101/2021.06.01.446543

4. M. V Jose, E.R. Morgado, R. Sanchez, T. Govezensky, The 24 possible algebraic representations of the standard genetic code in six or in three dimensions, Adv. Stud. Biol. 4 (2012) 119-152.PDF.

5. R. Sanchez. Symmetric Group of the Genetic-Code Cubes. Effect of the Genetic-Code Architecture on the Evolutionary Process MATCH Commun. Math. Comput. Chem. 79 (2018) 527-560.

See Also

codon_coord, base_coord and base2int.

Examples

## Load the MSA of Primate BRCA1 DNA repair genes
data("brca1_aln")

## Get the DNAStringSet for the first 33 codons and apply 'codon_matrix'
brca1 <- unmasked(brca1_aln)
brca1 <- subseq(brca1, start = 1, end = 33)
codon_matrix(brca1)

## Get back the alignment object and apply 'codon_matrix' gives us the 
## same result.
brca1 <- DNAMultipleAlignment(as.character(brca1))
codon_matrix(brca1)

---

Conserved and Non-conserved Regions from a MSA

Description

Returns the Conserved or the Non-conserved Regions from a MSA.

Usage

conserved_regions(x, ...)

## S4 method for signature 'Automorphism'
conserved_regions(
  x,
  conserved = TRUE,
  output = c("all_pairs", "unique_pairs", "unique")
)

## S4 method for signature 'AutomorphismList'
conserved_regions(
  x,
  conserved = TRUE,
  output = c("all_pairs", "unique_pairs", "unique"),
  num.cores = multicoreWorkers(),
  tasks = 0L,
  verbose = FALSE
)

## S4 method for signature 'AutomorphismByCoef'
conserved_regions(
  x,
  conserved = TRUE,
  output = c("all_pairs", "unique_pairs", "unique")
)

## S4 method for signature 'AutomorphismByCoefList'
conserved_regions(
  x,
  conserved = TRUE,
  output = c("all_pairs", "unique_pairs", "unique")
)

Arguments

x	A Automorphism-class, a AutomorphismList-class, a AutomorphismByCoef or a AutomorphismByCoefList class object.
...	Not in use.
conserved	Logical, Whether to return the conserved or the non-conserved regions.
output	A character string. Type of output.
num.cores, tasks	Integers. Argument num.cores denotes the number of cores to use, i.e. at most how many child processes will be run simultaneously (see bplapply function from BiocParallel package). Argument tasks denotes the number of tasks per job. value must be a scalar integer >= 0L. In this documentation a job is defined as a single call to a function, such as bplapply. A task is the division of the $X$ argument into chunks. When tasks == 0 (default), $X$ is divided as evenly as possible over the number of workers (see MulticoreParam from BiocParallel package).
verbose	logic(1). If TRUE, enable progress bar.

Value

A AutomorphismByCoef class object containing the requested regions.

Examples

## Load dataset
data("autm", package = "GenomAutomorphism")
conserved_regions(autm[1:3])
## Load automorphism found COVID datatset
data("covid_autm", package = "GenomAutomorphism")

## Conserved regions in the first 100 codons
conserv <- conserved_regions(covid_autm[1:100], output = "unique")
conserv

---

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

Description

This is a DNAMultipleAlignment carrying the pairwise sequence alignment of SARS coronavirus GZ02 (GenBank: AY390556.1: 265-13398_13398-21485) and Bat SARS-like coronavirus isolate bat-SL-CoVZC45 (GenBank: MG772933.1:265-1345513455-21542), complete genomes. The alignment is available at GitHub: https://github.com/genomaths/seqalignments/tree/master/COVID-19

Usage

data("covid_aln", package = "GenomAutomorphism")

Format

DNAMultipleAlignment class object.

Author(s)

Robersy Sanchez https://genomaths.com

See Also

brca1_aln, brca1_autm2, cyc_aln and covid_aln.

Examples

data("covid_aln", package = "GenomAutomorphism")
covid_aln

---

Automorphisms between DNA Sequences from two COVID-19 genomes

Description

This is a AutomorphismList object carrying a list of pairwise automorphisms between the SARS coronavirus GZ02 (GenBank: AY390556.1: 265-13398_13398-21485) and Bat SARS-like coronavirus isolate bat-SL-CoVZC45 (GenBank: KY417151.1: protein-coding regions). The pairwise DNA sequence alignment is available in the dataset named covid_aln and the automorphisms were estimated with function autZ64.

Usage

data("covid_autm", package = "GenomAutomorphism")

Format

AutomorphismList class object.

Author(s)

Robersy Sanchez https://genomaths.com

See Also

brca1_autm, brca1_autm2, cyc_autm, and covid_aln.

Examples

data("covid_autm", package = "GenomAutomorphism",
    envir = environment())
covid_autm

---

Multiple Sequence Alignment (MSA) of Primate Somatic Cytochrome C

Description

This is a DNAMultipleAlignment carrying a MSA of Primate Somatic Cytochrome C to be used in the examples provided for the package functions. The original file can be downloaded from GitHub at: https://bit.ly/3kdEAzs

Usage

data("cyc_aln", package = "GenomAutomorphism")

Format

DNAMultipleAlignment class object.

Author(s)

Robersy Sanchez https://genomaths.com

See Also

brca1_aln, brca1_aln2, covid_aln, and covid_aln.

Examples

data("cyc_aln", package = "GenomAutomorphism")
cyc_aln

---

Automorphisms between DNA Sequences from Primate Cytochrome C Genes

Description

This is a AutomorphismList object carrying a list of pairwise automorphisms between the DNA sequences from the MSA of Primate Somatic Cytochrome C to be used in the examples provided for the package functions. The automorphisms were estimated from the cyc_aln MSA with function autZ64.

Usage

data("cyc_autm", package = "GenomAutomorphism")

Format

AutomorphismList class object.

Author(s)

Robersy Sanchez https://genomaths.com

See Also

brca1_autm, brca1_autm2, covid_autm, and covid_aln.

Examples

data("cyc_autm", package = "GenomAutomorphism")
cyc_autm

---

Some Physicochemical Properties of DNA bases

Description

This data set carries some relevant physicochemical properties of the DNA bases. Available properties are:

"proton_affinity: "

It is an indicatio of the thermodynamic gradient between a molecule and the anionic form of that molecule upon removal of a proton from it (Wikipedia). The proton affinity values, given in kJ/mol, were taken from reference (1), also available in Wolfram Alpha at https://www.wolframalpha.com/ and in the cell phone App 'Wolfram Alpha'.. Reference (2) provides several measurements accomplished by several computational and experimental approaches.

"partition_coef: "

1-octanol/water partition coefficients, logP. In the physical sciences, a partition coefficient (P) or distribution coefficient (D) is the ratio of concentrations of a compound in a mixture of two immiscible solvents at equilibrium (3). The partition coefficient measures how hydrophilic ("water-loving") or hydrophobic ("water-fearing") a chemical substance is. Partition coefficients are useful in estimating the distribution of drugs within the body. Hydrophobic drugs with high octanol-water partition coefficients are mainly distributed to hydrophobic areas such as lipid bilayers of cells. Conversely, hydrophilic drugs (low octanol/water partition coefficients) are found primarily in aqueous regions such as blood serum. The partition coefficient values included here were taken from reference (1), also available in Wolfram Alpha at https://www.wolframalpha.com/ and in the cell phone App 'Wolfram Alpha'.

"dipole_moment: "

Dipole-dipole, dipole-induced-dipole and London force interactions among the bases in the helix are large, and make the free energy of the helix depend on the base composition and sequence. The dipole moment values were taken from reference (4). The dipole moment of DNA bases refers to the measure of polarity in the chemical bonds between atoms within the nucleobases. Dipole moments arise due to differences in electronegativity between the bonded atoms. In DNA bases, these dipole moments can influence the orientation of the bases when interacting with other molecules or surfaces, such as graphene/h-BN interfaces. The concept of dipole moments has been applied to analyze the electric moments of RNA-binding proteins, which can help identify DNA-binding proteins and provide insights into their mechanisms and prediction.

"tautomerization_energy: "

The term “tautomerism” is usually defined as structural isomerism with a low barrier to interconversion between the isomers, for example, the enol/imino forms for cytosine and guanine. Tautomerization is a process where the chemical structure of a molecule, such as DNA bases, undergoes a rearrangement of its atoms. This rearrangement results in the formation of different isomers, called tautomers, which can exist in solution or in a cell. The DNA bases can undergo tautomeric shifts, which can potentially contribute to mutagenic mispairings during DNA replication. The energy required for tautomerization of DNA bases is known as tautomerization energy. These values were taken from reference (2) and the value for each base corresponds to the average of the values estimated from different measurement approaches.

Usage

data("dna_phyche", package = "GenomAutomorphism")

Format

A data frame object.

References

1. Wolfram Research (2007), ChemicalData, Wolfram Language function, https://reference.wolfram.com/language/ref/ChemicalData.html (updated 2016).

2. Moser A, Range K, York DM. Accurate proton affinity and gas-phase basicity values for molecules important in biocatalysis. J Phys Chem B. 2010;114: 13911–13921. doi:10.1021/jp107450n.

3. Leo A, Hansch C, Elkins D. Partition coefficients and their uses. Chem Rev. 1971;71: 525–616. doi:10.1021/cr60274a001.

4. Vovusha H, Amorim RG, Scheicher RH, Sanyal B. Controlling the orientation of nucleobases by dipole moment interaction with graphene/h-BN interfaces. RSC Adv. Royal Society of Chemistry; 2018;8: 6527–6531. doi:10.1039/c7ra11664k.

Examples

data("dna_phyche", package = "GenomAutomorphism")
dna_phyche

## Select DNA base tautomerization energy
te <- as.list(dna_phyche$tautomerization_energy)
names(te) <- rownames(dna_phyche)

## Let's create DNAStringSet-class object
base <- DNAStringSet(x = c( seq1 ='ACGTGATCAAGT',
                            seq2 = 'GTGTGATCCAGT'))

dna_phychem(seqs = base, phychem = te,
            index_name = "Tautomerization-Energy")

---

DNA numerical matrix

Description

This function applies the numerical indices representing various physicochemical and biochemical properties of DNA bases. As results, DNA sequences are represented as numerical vectors which can be subject of further downstream statistical analysis and digital signal processing.

Usage

dna_phychem(seqs, ...)

## S4 method for signature 'character'
dna_phychem(
  seqs,
  phychem = list(A = NULL, T = NULL, C = NULL, G = NULL, N = NULL)
)

## S4 method for signature 'DNAStringSet_OR_DNAMultipleAlignment'
dna_phychem(
  seqs,
  phychem = list(A = NULL, T = NULL, C = NULL, G = NULL, N = NULL),
  index_name = NULL,
  ...
)

Arguments

seqs	A character string, a DNAStringSet or a DNAMultipleAlignment class object carrying the DNA pairwise alignment of two sequences.
...	Not in use.
phychem	A list of DNA bases physicochemical properties, e.g., like those provided in dna_phyche.
index_name	Optional. Name of breve description of the base physicochemical property applied to represent the DNA sequence.

Value

A MatrixSeq-class object.

Author(s)

Robersy Sanchez https://genomaths.com

See Also

peptide_phychem_index

Examples

## Let's create DNAStringSet-class object 
base <- DNAStringSet(x = c( seq1 ='ACGTGATCAAGT', 
                            seq2 = 'GTGTGATCCAGT', 
                            seq3 = 'TCCTGATCAGGT'))


dna_phychem(seqs = base,
            phychem = list('A' = 0.87, 'C' = 0.88, 'T' = 0.82,
                            'G' = 0.89, 'N' = NA),
            index_name = "Proton-Affinity")

---

DNA base/codon sequence and coordinates represented on a given Abelian group.

Description

Given a string denoting a codon or base from the DNA (or RNA) alphabet and a genetic-code Abelian group as given in reference (1), this function returns an object from CodonGroup-class carrying the DNA base/codon sequence and coordinates represented on the given Abelian group.

Usage

get_coord(x, ...)

## S4 method for signature 'BaseGroup_OR_CodonGroup'
get_coord(x, output = c("all", "matrix.list"))

## S4 method for signature 'DNAStringSet_OR_NULL'
get_coord(
  x,
  output = c("all", "matrix.list"),
  base_seq = TRUE,
  filepath = NULL,
  cube = "ACGT",
  group = "Z4",
  start = NA,
  end = NA,
  chr = 1L,
  strand = "+"
)

Arguments

x	An object from a BaseGroup-class, CodonGroup-class, DNAStringSet or DNAMultipleAlignment class carrying the DNA pairwise alignment of two sequences. Objects from BaseGroup-class and CodonGroup-class are generated with functions: base_coord and codon_coord, respectively.
...	Not in use.
output	See 'Value' section.
base_seq	Logical. Whether to return the base or codon coordinates on the selected Abelian group. If codon coordinates are requested, then the number of the DNA bases in the given sequences must be multiple of 3.
filepath	A character vector containing the path to a file in fasta format to be read. This argument must be given if codon & base arguments are not provided.
cube	A character string denoting one of the 24 Genetic-code cubes, as given in references (2 2 3).
group	A character string denoting the group representation for the given base or codon as shown in reference (1).
start, end, chr, strand	Optional parameters required to build a GRanges-class. If not provided the default values given for the function definition will be used.

Details

Symbols '-' and 'N' usually found in DNA sequence alignments to denote gaps and missing/unknown bases are represented by the number: '-1' on Z4 and '0' in Z5. In Z64 the symbol 'NA' will be returned for codons including symbols '-' and 'N'.

Although the CodonGroup-class object returned by functions codon_coord and base_coord are useful to store genomic information, the base and codon coordinates are not given on them as numeric magnitudes. Function get_coord provides the way to get the coordinates in a numeric object in object from and still to preserve the base/codon sequence information.

Value

An object from CodonGroup-class class is returned when output = 'all'. This has two slots, the first one carrying a list of matrices and the second one carrying the codon/base sequence information. That is, if x is an object from CodonGroup-class class, then a list of matrices of codon coordinate can be retrieved as x@CoordList and the information on the codon sequence as x@SeqRanges.

if output = 'matrix.list', then an object from MatrixList class is returned.

Examples

## Load a pairwise alignment
data("aln", package = "GenomAutomorphism")
aln

## DNA base representation in the Abelian group Z5
coord <- get_coord(
    x = aln,
    cube = "ACGT",
    group = "Z5"
)
coord ## A list of vectors

## Extract the coordinate list
coordList(coord)

## Extract the sequence list
seqRanges(coord)

## DNA codon representation in the Abelian group Z64
coord <- get_coord(
    x = aln,
    base_seq = FALSE,
    cube = "ACGT",
    group = "Z64"
)
coord

## Extract the coordinate list
coordList(coord)

## Extract the sequence list
seqRanges(coord)

---

Get Mutation Score from an AAindex or a Mutation/Distance Matrix

Description

This function is applied to get the mutation or contact potential scores representing the similarity/distance between amino acids corresponding to substitution mutations. The scores are retrieved from a mutation matrix or a statistical protein contact potentials matrix from AAindex (ver.9.2).

Alternatively, the mutation scores can be estimated based on an user mutation matrix, for example, see aminoacid_dist and codon_dist_matrix.

Usage

get_mutscore(aa1, aa2, ...)

## S4 method for signature 'character,character'
get_mutscore(
  aa1,
  aa2,
  acc = NULL,
  aaindex = NULL,
  mutmat = NULL,
  alphabet = c("AA", "DNA"),
  num.cores = 1L,
  tasks = 0L,
  verbose = FALSE,
  ...
)

## S4 method for signature 'BaseSeq,missing'
get_mutscore(
  aa1,
  aa2,
  acc = NULL,
  aaindex = NULL,
  mutmat = NULL,
  alphabet = c("AA", "DNA"),
  stat = mean,
  numcores = 1L,
  num.cores = 1L,
  tasks = 0L,
  output = c("dist", "matrix", "vector"),
  na.rm = TRUE,
  verbose = TRUE,
  ...
)

## S4 method for signature 'DNAStringSet,missing'
get_mutscore(
  aa1,
  aa2,
  acc = NULL,
  aaindex = NULL,
  mutmat = NULL,
  alphabet = c("AA", "DNA"),
  stat = mean,
  num.cores = 1L,
  tasks = 0L,
  verbose = TRUE,
  output = c("dist", "matrix", "vector"),
  na.rm = TRUE,
  ...
)

## S4 method for signature 'DNAMultipleAlignment,missing'
get_mutscore(
  aa1,
  aa2,
  acc = NULL,
  aaindex = NULL,
  mutmat = NULL,
  alphabet = c("AA", "DNA"),
  stat = mean,
  num.cores = 1L,
  tasks = 0L,
  verbose = TRUE,
  output = c("dist", "matrix", "vector"),
  na.rm = TRUE,
  ...
)

Arguments

aa1, aa2	A simple character representing an amino acids or a character string of letter from the amino acid alphabet or base-triplets from the DNA/RNA alphabet. If aa1 is an object from any of the classes: BaseSeq, DNAStringSet, or DNAMultipleAlignment, then argument aa2 is not required.
...	Not in use.
acc	Accession id for a specified mutation or contact potential matrix.
aaindex	Database where the requested accession id is locate. The possible values are: "aaindex2" or "aaindex3".
mutmat	A mutation or any score matrix provided by the user.
alphabet	Whether the alphabet is from the 20 amino acid (AA) or four (DNA)/RNA base alphabet. This would prevent mistakes, i.e., the strings "ACG" would be a base-triplet on the DNA alphabet or simply the amino acid sequence of alanine, cysteine, and glutamic acid.
num.cores, tasks	Parameters for parallel computation using package BiocParallel-package: the number of cores to use, i.e. at most how many child processes will be run simultaneously (see bplapply and the number of tasks per job (only for Linux OS).
verbose	Optional. Only if num.cores > 1. If TRUE, prints the function log to stdout.
stat	Statistic that will be used to summarize the scores of the DNA sequences provided. Only if aa1 is an object from any of the classes: BaseSeq, DNAStringSet, or DNAMultipleAlignment.
numcores	An integer to setup the number of parallel workers via makeCluster.
output	Optional. Class of the returned object. Only if aa1 is an object from any of the classes: BaseSeq, DNAStringSet, or DNAMultipleAlignment.
na.rm	a logical evaluating to TRUE or FALSE indicating whether NA values should be stripped before the computation proceeds.

Details

If a score matrix is provided by the user, then it must be a symmetric matrix 20x20.

Value

A single numeric score or a numerical vector, or if aa1 is an object from any of the classes: BaseSeq, DNAStringSet, or DNAMultipleAlignment, then depending on the user selection the returned object will be:

1. A lower diagonal numerical vector of the sequence pairwise scores.

2. A dist-class object.

3. A whole score matrix.

Author(s)

Robersy Sanchez https://genomaths.com

See Also

aa_mutmat, aaindex2 and aaindex3.

Examples

## A single amino acids substitution mutation
get_mutscore("A", "C", acc = "MIYS930101", aaindex = "aaindex2")

## A tri-peptide mutation
get_mutscore(aa1 = "ACG", aa2 = "ATG", acc = "MIYS930101",
            aaindex = "aaindex2", alphabet = "AA")

## A single base-triple mutation, i.e., a single amino acid substitution 
## mutation
get_mutscore(aa1 = "ACG", aa2 = "CTA", acc = "MIYS930101",
            aaindex = "aaindex2", alphabet = "DNA")

## Peptides can be also written as:
get_mutscore(aa1 = c("A","C","G"), aa2 = c("C","T","A"), 
            acc = "MIYS930101", aaindex = "aaindex2", alphabet = "AA")

---

Get Automorphisms

Description

For the sake of saving memory, each Automorphism-class objects is stored in an AutomorphismList-class, which does not inherits from a GRanges-class.

Usage

getAutomorphisms(x, ...)

## S4 method for signature 'AutomorphismList'
getAutomorphisms(x)

## S4 method for signature 'list'
getAutomorphisms(x)

## S4 method for signature 'DataFrame_OR_data.frame'
getAutomorphisms(x)

Arguments

x	An AutomorphismList-class.
...	Not in use.

Details

This function just transform each Automorphism-class object into an object from the same class but now inheriting from a GRanges-class.

Value

This function returns an AutomorphismList-class object as a list of Automorphism-class objects, which inherits from GRanges-class objects.

An AutomorphismList-class

An Automorphism-class

Examples

## Load a dataset
data("autm", package = "GenomAutomorphism")
aut <- mcols(autm)
aut ## This a DataFrame object

## The natural ranges for the sequence (from 1 to length(aut)) are added
getAutomorphisms(aut)

## A list of automorphisms
aut <- list(aut, aut)
getAutomorphisms(aut)

## Automorphism-class inherits from 'GRanges-class'
aut <- as(autm, "GRanges")
as(aut, "Automorphism")

---

Get the Coordinate Representation from DNA Sequences on Specified Abelian Group

Description

Extract the Coordinate Representation from DNA Sequences on Specified Abelian Group.

Usage

matrices(x, ...)

## S4 method for signature 'MatrixList'
matrices(x)

## S4 method for signature 'CodonSeq'
matrices(x)

## S4 method for signature 'DNAStringSet_OR_NULL'
matrices(
  x,
  base_seq = TRUE,
  filepath = NULL,
  cube = "ACGT",
  group = c("Z4", "Z5", "Z64", "Z125", "Z4^3", "Z5^3"),
  start = NA,
  end = NA,
  chr = 1L,
  strand = "+"
)

Arguments

x	An object from a DNAStringSet or DNAMultipleAlignment class carrying the DNA pairwise alignment of two sequences.
...	Not in use.
base_seq	Logical. Whether to return the base or codon coordinates on the selected Abelian group. If codon coordinates are requested, then the number of the DNA bases in the given sequences must be multiple of 3.
filepath	A character vector containing the path to a file in fasta format to be read. This argument must be given if codon & base arguments are not provided.
cube	A character string denoting one of the 24 Genetic-code cubes, as given in references (2-3).
group	A character string denoting the group representation for the given base or codon as shown in reference (1).
start, end, chr, strand	Optional parameters required to build a GRanges-class. If not provided the default values given for the function definition will be used.

Details

These are alternative ways to get the list of matrices of base/codon coordinate and the information on the codon sequence from CodonSeq and MatrixList class objects. These functions can either take the output from functions base_coord and matrices or to operate directly on a DNAStringSet or to retrieve the a DNA sequence alignment from a file.

base_seq parameter will determine whether to return the matrices of coordinate for a DNA or codon sequence. While in function seqranges, granges parameter will determine whether to return a GRanges-class object or a DataFrame.

Value

The a list of vectors (group = c("Z4", "Z5", "Z64", "Z125") or a list of matrices (group = ("Z4^3", "Z5^3")) carrying the coordinate representation on the specified Abelian group.

Author(s)

Robersy Sanchez https://genomaths.com

References

1. Robersy Sanchez, Jesus Barreto (2021) Genomic Abelian Finite Groups. doi: 10.1101/2021.06.01.446543

2. M. V Jose, E.R. Morgado, R. Sanchez, T. Govezensky, The 24 possible algebraic representations of the standard genetic code in six or in three dimensions, Adv. Stud. Biol. 4 (2012) 119-152.PDF.

3. R. Sanchez. Symmetric Group of the Genetic-Code Cubes. Effect of the Genetic-Code Architecture on the Evolutionary Process MATCH Commun. Math. Comput. Chem. 79 (2018) 527-560.

See Also

Symmetric Group of the Genetic-Code Cubes.

Examples

## Load a pairwise alignment
data("aln", package = "GenomAutomorphism")
aln

## Coordinate representation of the aligned sequences on "Z4".
## A list of vectors
matrices(
    x = aln,
    base_seq = TRUE,
    filepath = NULL,
    cube = "ACGT",
    group = "Z4",
)

## Coordinate representation of the aligned sequences on "Z4".
## A list of matrices
matrices(
    x = aln,
    base_seq = FALSE,
    filepath = NULL,
    cube = "ACGT",
    group = "Z5^3",
)

---

Modulo Operation

Description

Integer remainder of the division of the integer n by m: n mod m.

Usage

mod(n, m, ...)

## S4 method for signature 'matrix,numeric'
mod(n, m)

Arguments

n	A numeric vector (preferably of integers), a matrix where each element can be reduced to integers.
m	An integer vector (positive, zero, or negative).
...	Not in use.

Value

An element of x, an Automorphism-class object.

Author(s)

Robersy Sanchez (https://genomaths.com).

Examples

## Example 1
## Build a matrix 'n' and set a vector of integers 'm'
n <- diag(x=1, nrow = 4, ncol = 4) * c(43,125,2,112)
m <- c(64,4,4,64)

## Operation n mod m 
mod(n = n, m = m)

## Or simply:
n %% m

## Example 2
m <- matrix(c(8,2,3, 11,12,13), nrow = 2)
m

m %% 4

---

Modular System of Linear Equation Solver (MLE)

Description

If $a, b$, and $c$ are integer vectors, this function try to find, at each coordinate, the solution of the MLE $a x = b$ mod $n$. If the MLE $a x = b mod n$ has not solutions (see modlin), the value reported for the coordinate will be 0 and the corresponding translation.

Usage

modlineq(a, b, n, no.sol = 0L)

Arguments

a	An integer or a vector of integers.
b	An integer or a vector of integers.
n	An integer or a vector of integers.
no.sol	Values to return when the equation is not solvable or yield the value 0. Default is 0.

Details

For $a, b$, and $c$ integer scalars, it is just a wrapper function to call modlin.

Value

If the solution is exact, then a numerical vector will be returned, otherwise, if there is not exact solution for some coordinate, the a list carrying the element on the diagonal matrix and a translation vector will be returned.

Examples

## Set the vector x, y, and m.
x <- c(9,32,24,56,60,27,28,5)
y <-  c(8,1,0,56,60,0,28,2)
modulo <- c(64,125,64,64,64,64,64,64)

## Try to solve the modular equation a x = b mod n
m <- modlineq(a = x, b = y, n = modulo)
m

## Or in matrix form 
diag(m)

## The reverse mapping is an affine transformation
mt <- modlineq(a = y, b = x, n = modulo, no.sol = 1L)
mt

## That is, vector 'x' is revovered with the transformaiton
(y %*% diag(mt$diag) + mt$translation) %% modulo

# Or
cat("\n---- \n")

(y %*% diag(mt$diag) + mt$translation) %% modulo == x

---

Classification of DNA base mutations

Description

Each DNA/RNA base can be classified into three main classes according to three criteria (1): number of hydrogen bonds (strong-weak), chemical type (purine-pyrimidine), and chemical groups (amino versus keto). Each criterion produces a partition of the set of bases: 1) According to the number of hydrogen bonds (on DNA/RNA double helix): strong $S=(C,G)$ (three hydrogen bonds) and weak $W=(A,U)$ (two hydrogen bonds). According to the chemical type: purines $R=(A, G)$ and pyrimidines $Y=(C,U)$. 3). According to the presence of amino or keto groups on the base rings: amino $M=(C,A)$ and keto $K=(G,U)$. So, each mutational event can be classified as according to the type of involved in it (2).

Usage

mut_type(x, y)

Arguments

x, y	Character strings denoting DNA bases

Value

A character string of same length of 'x' and 'y'.

References

1. A. Cornish-Bowden, Nomenclature for incompletely specified bases in nucleic acid sequences: recommendations 1984, Nucleic Acids Res. 13 (1985) 3021-3030.

2. MA.A. Jimenez-Montano, C.R. de la Mora-Basanez, T. Poschel, The hypercube structure of the genetic code explains conservative and non-conservative aminoacid substitutions in vivo and in vitro, Biosystems. 39 (1996) 117-125.

Examples

## Mutation type 'R'
mut_type("A", "G")

## Mutation type 'M'
mut_type("A", "C")

## Mutation type 'W'
mut_type("A", "T")

## Mutation type 'S'
mut_type("G", "C")

---

Amino acid numerical matrix

Description

This function applies numerical indices representing various physicochemical and biochemical properties of amino acids and pairs of amino acids to DNA protein-coding or to aminoacid sequences. As results, DNA protein-coding or the aminoacid sequences are represented as numerical vectors which can be subject of further downstream statistical analysis and digital signal processing.

Usage

peptide_phychem_index(aa, ...)

## S4 method for signature 'character'
peptide_phychem_index(
  aa,
  acc = NULL,
  aaindex = NA,
  userindex = NULL,
  alphabet = c("AA", "DNA"),
  genetic.code = getGeneticCode("1"),
  no.init.codon = FALSE,
  if.fuzzy.codon = "error",
  ...
)

## S4 method for signature 'DNAStringSet_OR_DNAMultipleAlignment'
peptide_phychem_index(
  aa,
  acc = NULL,
  aaindex = NA,
  userindex = NULL,
  alphabet = c("AA", "DNA"),
  genetic.code = getGeneticCode("1"),
  no.init.codon = FALSE,
  if.fuzzy.codon = "error",
  num.cores = 1L,
  tasks = 0L,
  verbose = FALSE,
  ...
)

Arguments

aa	A character string, a DNAStringSet or a DNAMultipleAlignment class object carrying the DNA pairwise alignment of two sequences.
...	Not in use.
acc	Accession id for a specified mutation or contact potential matrix.
aaindex	Database where the requested accession id is locate and from where the aminoacid indices can be obtained. The possible values are: "aaindex2" or "aaindex3".
userindex	User provided aminoacid indices. This can be a numerical vector or a matrix (20 x 20). If a numerical matrix is provided, then the aminoacid indices are computes as column averages.
alphabet	Whether the alphabet is from the 20 aminoacid (AA) or four (DNA)/RNA base alphabet. This would prevent mistakes, i.e., the strings "ACG" would be a base-triplet on the DNA alphabet or simply the amino acid sequence of alanine, cysteine, and glutamic acid.
genetic.code, no.init.codon, if.fuzzy.codon	The same as given in function translation.
num.cores, tasks	Parameters for parallel computation using package BiocParallel-package: the number of cores to use, i.e. at most how many child processes will be run simultaneously (see bplapply and the number of tasks per job (only for Linux OS).
verbose	If TRUE, prints the function log to stdout.

Details

If a DNA sequence is given, then it is assumed that it is a DNA base-triplet sequence, i.e., the base sequence must be multiple of 3.

Errors can be originated if the given sequences carry letter which are not from the DNA or aminoacid alphabet.

Value

Depending on the user specifications, a mutation or contact potential matrix, a list of available matrices (indices) ids or index names can be returned. More specifically:

aa_mutmat:

Returns an aminoacid mutation matrix or a statistical protein contact potentials matrix.

aa_index:

Returns the specified aminoacid physicochemical indices.

Author(s)

Robersy Sanchez https://genomaths.com

Examples

## Let's create DNAStringSet-class object
base <- DNAStringSet(x = c( seq1 ='ACGTCATAAAGT',
                            seq2 = 'GTGTAATACAGT',
                            seq3 = 'TCCTCATAAGGT'))

## The stop condon 'TAA' yields NA
aa <- peptide_phychem_index(base, acc = "EISD840101")
aa

## Description of the physicochemical index
slot(aa, 'phychem')

## Get the aminoacid sequences. The stop codon 'TAA' is replaced by '*'.
slot(aa, 'seqs')


aa <- peptide_phychem_index(base, acc = "MIYS850103", aaindex = "aaindex3")
aa

## Description of the physicochemical index
slot(aa, 'phychem')

---

Get DNA sequence Ranges and Coordinates representation on a given Abelian Group

Description

Extract the gene ranges and coordinates from a pairwise alignment of codon/base sequences represented on a given Abelian group.

Usage

seqranges(x, ...)

## S4 method for signature 'CodonSeq'
seqranges(x, granges = TRUE)

## S4 method for signature 'DNAStringSet_OR_NULL'
seqranges(
  x,
  granges = TRUE,
  base_seq = TRUE,
  filepath = NULL,
  start = NA,
  end = NA,
  chr = 1L,
  strand = "+"
)

Arguments

x	An object from a DNAStringSet or DNAMultipleAlignment class carrying the DNA pairwise alignment of two sequences.
...	Not in use.
granges	Logical. Whether to return a GRanges-class object or a DataFrame.
base_seq	Logical. Whether to return the base or codon coordinates on the selected Abelian group. If codon coordinates are requested, then the number of the DNA bases in the given sequences must be multiple of 3.
filepath	A character vector containing the path to a file in fasta format to be read. This argument must be given if codon & base arguments are not provided.
start, end, chr, strand	Optional parameters required to build a GRanges-class. If not provided the default values given for the function definition will be used.

Details

This function provide an alternative way to get the codon coordinate and the information on the codon sequence from a CodonSeq class objects. The function can either take the output from functions codon_coord or to operate directly on a DNAStringSet or to retrieve the a DNA sequence alignment from a file.

Value

A GRanges-class

Author(s)

Robersy Sanchez https://genomaths.com

References

1. Robersy Sanchez, Jesus Barreto (2021) Genomic Abelian Finite Groups. doi:10.1101/2021.06.01.446543

2. M. V Jose, E.R. Morgado, R. Sanchez, T. Govezensky, The 24 possible algebraic representations of the standard genetic code in six or in three dimensions, Adv. Stud. Biol. 4 (2012) 119-152.PDF.

3. R. Sanchez. Symmetric Group of the Genetic-Code Cubes. Effect of the Genetic-Code Architecture on the Evolutionary Process MATCH Commun. Math. Comput. Chem. 79 (2018) 527-560.

See Also

matrices, codon_coord, and base_coord.

Examples

## Load a pairwise alignment
data("aln", package = "GenomAutomorphism")
aln

## A GRanges object carrying the aligned DNA sequence.
seqranges(
    x = aln,
    base_seq = TRUE,
    filepath = NULL,
)

## A GRanges object carrying the aligned codon sequence.
seqranges(
    x = aln,
    base_seq = FALSE,
    filepath = NULL,
)

---

Apply a function over a list-like object preserving its attributes

Description

This function apply a function over a list-like object preserving its attributes and simplify (if requested) the list as sapply function does. slapply returns a list of the same length as 'x', each element of which is the result of applying FUN to the corresponding element of 'x'.

Usage

slapply(
  x,
  FUN,
  keep.attr = FALSE,
  class = NULL,
  simplify = TRUE,
  USE.NAMES = TRUE,
  ...
)

Arguments

x	A list-like or vector-like object.
FUN, ...	The same as described in lapply.
keep.attr	Logic. If TRUE, then the original attributes from 'x' are preserved in the returned list. Default is FALSE.
class	Name of the class to which the returned list belongs to. Default is NULL.
simplify, USE.NAMES	The same as described in sapply.

Value

Same as in ?base::lapply if keep.attr = FALSE. Otherwise same values preserving original attributes from 'x'.

Author(s)

Robersy Sanchez (https://genomaths.com).

See Also

lapply and sapply

Examples

## Create a list
x <- list(a = seq(10), beta = exp(seq(-3, 3)), 
          logic = c(TRUE, FALSE, FALSE, TRUE))
class(x) <- "nice"

## To compute the list mean for each list element using 'base::lapply'
class(slapply(x, mean, simplify = FALSE))

## Simply 'base::lapply' preserving attributes
slapply(x, mean, keep.attr = TRUE, simplify = FALSE)

## To preserve attributes and simplify
slapply(x, mean, keep.attr = TRUE, simplify = TRUE)

---

Sorting GRanges-class objects

Description

Sorts a GRanges-class objects by seqname (chromosome), start, and position.

Usage

sortByChromAndStart(x)

sortByChromAndEnd(x)

Arguments

x	GRanges object

Details

Objects that inherits from a GRanges-class can be sorted as well.

Value

GRanges-class object or from the original object class.

Examples

GR <- as(c("chr2:1-1", "chr1:1-1"), "GRanges")
GR <- sortByChromAndStart(GR)

---

String to Character

Description

A simple function to transform a string into character vector.

Usage

str2chr(x, split = "", ...)

## S4 method for signature 'character'
str2chr(x, split = "", ...)

## S4 method for signature 'list'
str2chr(x, split = "", num.cores = 1L, tasks = 0L, verbose = FALSE, ...)

Arguments

x	A character string or a list/vector of character strings.
split	The same as in strsplit
...	Further parameters for strsplit.
num.cores, tasks	Parameters for parallel computation using package BiocParallel-package: the number of cores to use, i.e. at most how many child processes will be run simultaneously (see bplapply and the number of tasks per job (only for Linux OS).
verbose	If TRUE, prints the function log to stdout.

Value

A character string

Author(s)

Robersy Sanchez https://genomaths.com

Examples

## A character string
str2chr("ATCAGCGGGATCTT")

## A list of character strings
str2chr(list(str1 = "ATCAGCGGGATCTT", str2 = "CTTCTTCGTCAGGC"))

---