Base coordinates on a given a given Abelian group representation.
Source:R/base_coord.R
base_coord.RdGiven 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
base_coord(base = NULL, filepath = NULL, cube = "ACGT", group = "Z4", ...)
# S4 method for 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 = "+"
)Arguments
- base
An object from a
DNAStringSetorDNAMultipleAlignmentclass 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.
- 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 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).
References
Robersy Sanchez, Jesus Barreto (2021) Genomic Abelian Finite Groups. doi:10.1101/2021.06.01.446543
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.
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.
Author
Robersy Sanchez https://genomaths.com
Examples
## Example 1. Let's get the base coordinates for codons "ACG"
## and "TGC":
x0 <- c("ACG", "TGC")
x1 <- DNAStringSet(x0)
x1
#> DNAStringSet object of length 2:
#> width seq
#> [1] 3 ACG
#> [2] 3 TGC
## Get the base coordinates on cube = "ACGT" on the Abelian group = "Z4"
base_coord(x1, cube = "ACGT", group = "Z4")
#> BaseGroup object with 3 ranges and 4 metadata columns:
#> seqnames ranges strand | seq1 seq2 coord1 coord2
#> <Rle> <IRanges> <Rle> | <character> <character> <numeric> <numeric>
#> [1] 1 1 + | A T 0 3
#> [2] 1 2 + | C G 1 2
#> [3] 1 3 + | G C 2 1
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
## Example 2. Load a pairwise alignment
data(aln, package = "GenomAutomorphism")
aln
#> DNAStringSet object of length 2:
#> width seq
#> [1] 51 ACCTATGTTGGTATT---GCGCTCCAACTCCTTGGCTCTAGCTCACTACAT
#> [2] 51 ATCTATGTTGGTATTACGACGCTCCAATTCCTTGGGTCC------CTCCTT
## DNA base representation in the Abelian group Z4
bs_cor <- base_coord(
base = aln,
cube = "ACGT"
)
bs_cor
#> BaseGroup object with 51 ranges and 4 metadata columns:
#> seqnames ranges strand | seq1 seq2 coord1 coord2
#> <Rle> <IRanges> <Rle> | <character> <character> <numeric> <numeric>
#> [1] 1 1 + | A A 0 0
#> [2] 1 2 + | C T 1 3
#> [3] 1 3 + | C C 1 1
#> [4] 1 4 + | T T 3 3
#> [5] 1 5 + | A A 0 0
#> ... ... ... ... . ... ... ... ...
#> [47] 1 47 + | T T 3 3
#> [48] 1 48 + | A C 0 1
#> [49] 1 49 + | C C 1 1
#> [50] 1 50 + | A T 0 3
#> [51] 1 51 + | T T 3 3
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
## Example 3. DNA base representation in the Abelian group Z5
bs_cor <- base_coord(
base = aln,
cube = "ACGT",
group = "Z5"
)
bs_cor
#> BaseGroup object with 51 ranges and 4 metadata columns:
#> seqnames ranges strand | seq1 seq2 coord1 coord2
#> <Rle> <IRanges> <Rle> | <character> <character> <numeric> <numeric>
#> [1] 1 1 + | A A 1 1
#> [2] 1 2 + | C T 2 4
#> [3] 1 3 + | C C 2 2
#> [4] 1 4 + | T T 4 4
#> [5] 1 5 + | A A 1 1
#> ... ... ... ... . ... ... ... ...
#> [47] 1 47 + | T T 4 4
#> [48] 1 48 + | A C 1 2
#> [49] 1 49 + | C C 2 2
#> [50] 1 50 + | A T 1 4
#> [51] 1 51 + | T T 4 4
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths