seqranges: Get DNA sequence Ranges and Coordinates representation on a...

In genomaths/GenomAutomorphism: Compute the automorphisms between DNA's Abelian group representations

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,
)

genomaths/GenomAutomorphism documentation built on Dec. 12, 2024, 2:12 p.m.