A class definition to store codon coordinates given in the Abelian group and the codon sequence.
Source:R/allClasses.R
CodonSeq.RdAn objects from 'CodonSeq' or 'MatrixList' class is returned
by function get_coord. This object will store the coordinate
of each sequence in a list of 3D-vectors or a list of vectors located in
the slot named 'CoordList'. The original codon sequence (if provided) will
be stored in the slot named 'SeqRanges'.
Usage
coordList(x)
# S4 method for CodonSeq
coordList(x)
seqRanges(x)
# S4 method for CodonSeq
seqRanges(x)Examples
## Load a DNA sequence alignment
data("aln", package = "GenomAutomorphism")
## Get base coordinates on 'Z5'
coord <- get_coord(
x = aln,
cube = "ACGT",
group = "Z5"
)
coordList(coord)
#> $coord1
#> [1] 1 2 2 4 1 4 3 4 4 3 3 4 1 4 4 0 0 0 3 2 3 2 4 2 2 1 1 2 4 2 2 4 4 3 3 2 4 2
#> [39] 4 1 3 2 4 2 1 2 4 1 2 1 4
#>
#> $coord2
#> [1] 1 4 2 4 1 4 3 4 4 3 3 4 1 4 4 1 2 3 1 2 3 2 4 2 2 1 1 4 4 2 2 4 4 3 3 3 4 2
#> [39] 2 0 0 0 0 0 0 2 4 2 2 4 4
#>
## Load a DNA sequence alignment
data("aln", package = "GenomAutomorphism")
## Get base coordinates on 'Z5'
coord <- get_coord(
x = aln,
cube = "ACGT",
group = "Z5"
)
seqRanges(coord)
#> GRanges object with 51 ranges and 2 metadata columns:
#> seqnames ranges strand | seq1 seq2
#> <Rle> <IRanges> <Rle> | <character> <character>
#> [1] 1 1 + | A A
#> [2] 1 2 + | C T
#> [3] 1 3 + | C C
#> [4] 1 4 + | T T
#> [5] 1 5 + | A A
#> ... ... ... ... . ... ...
#> [47] 1 47 + | T T
#> [48] 1 48 + | A C
#> [49] 1 49 + | C C
#> [50] 1 50 + | A T
#> [51] 1 51 + | T T
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths