A Convenient Class to Store a Codon Coordinate in given Genetic Code cube.

A CodonMatrix is the object created by function codon_matrix

Usage

CodonMatrix(object, group, cube, seq_alias = NULL)

Arguments

object

A GRanges-class object.

group

The name of the base group, 'Z4' or 'Z5'.

cube

The name of the genetic-code cube applied to get the codon coordinates.

seq_alias

The 'alias' given to the codon sequence.

Value

A 'CodonMatrix' class object

See also

base_coord and codon_coord.

Examples

## CodonMatrix is generated by function 'codon_matrix' (inside a
## ListCodonMatrix-class object)
## Let's create DNAStringSet-class object
base <- DNAStringSet(x = c(S1 = 'ACGTGATCAAGT'))

x1 <- codon_matrix(base)
x1
#> ListCodonMatrix object of length: 4
#> Seq.Alias: codon.1 codon.2 codon.3 codon.4 ...
#> 
#> ------- 
#> $codon.1
#> CodonMatrix object with 3 ranges and 1 metadata column:
#>       seqnames    ranges strand |        S1
#>          <Rle> <IRanges>  <Rle> | <numeric>
#>   [1]        1       1-3      + |         0
#>   [2]        1       1-3      + |         1
#>   [3]        1       1-3      + |         2
#>   -------
#>   seqinfo: 1 sequence from an unspecified genome; no seqlengths
#> 
#> 
#> $codon.2
#> CodonMatrix object with 3 ranges and 1 metadata column:
#>     seqnames    ranges strand |        S1
#>        <Rle> <IRanges>  <Rle> | <numeric>
#>   4        1       4-6      + |         3
#>   5        1       4-6      + |         2
#>   6        1       4-6      + |         0
#>   -------
#>   seqinfo: 1 sequence from an unspecified genome; no seqlengths
#> 
#> ...
#> 
#> <2 more CodonMatrix element(s)>
#> Three slots: 'DataList', 'group', 'cube' & 'seq_alias'
#> ------- 

## Extract the first element
x1[1]
#> ListCodonMatrix object of length: 1
#> Seq.Alias: codon.1 codon.2 codon.3 codon.4 
#> 
#> ------- 
#> $codon.1
#> CodonMatrix object with 3 ranges and 1 metadata column:
#>       seqnames    ranges strand |        S1
#>          <Rle> <IRanges>  <Rle> | <numeric>
#>   [1]        1       1-3      + |         0
#>   [2]        1       1-3      + |         1
#>   [3]        1       1-3      + |         2
#>   -------
#>   seqinfo: 1 sequence from an unspecified genome; no seqlengths
#> Three slots: 'DataList', 'group', 'cube' & 'seq_alias'
#> ------- 
x1$codon.1
#> CodonMatrix object with 3 ranges and 1 metadata column:
#>       seqnames    ranges strand |        S1
#>          <Rle> <IRanges>  <Rle> | <numeric>
#>   [1]        1       1-3      + |         0
#>   [2]        1       1-3      + |         1
#>   [3]        1       1-3      + |         2
#>   -------
#>   seqinfo: 1 sequence from an unspecified genome; no seqlengths
x1[[1]]
#> CodonMatrix object with 3 ranges and 1 metadata column:
#>       seqnames    ranges strand |        S1
#>          <Rle> <IRanges>  <Rle> | <numeric>
#>   [1]        1       1-3      + |         0
#>   [2]        1       1-3      + |         1
#>   [3]        1       1-3      + |         2
#>   -------
#>   seqinfo: 1 sequence from an unspecified genome; no seqlengths