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Distance Between Aminoacids in Terms of Codon Distance

Source: R/aminoacid_dist.R
aminoacid_dist.Rd

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 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 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 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 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.

Value

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

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.

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)
#>       A.A       *.A       L.M       T.T       H.D       M.M       C.- 
#> 0.1041667 2.0000000 0.4791667 0.1041667 0.3125000 0.0000000 2.0000000 

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

aminoacid_dist(aa1 = aa)
#>       A.A       *.A       L.M       T.T       H.D       M.M       C.- 
#> 0.1041667 2.0000000 0.4791667 0.1041667 0.3125000 0.0000000 2.0000000 

## Let's select cube "GCAT" and group "Z5"
aminoacid_dist(aa1 = aa, group = "Z5", cube = "TCGA")
#>        A.A        *.A        L.M        T.T        H.D        M.M        C.- 
#> 0.06666667 4.00000000 0.50000000 0.06666667 0.22000000 0.00000000 4.00000000