Automorphisms between DNA Primate BRCA1 Genes Grouped by Coefficients
Source:R/data_autby_coef.R
autby_coef.RdThis is a AutomorphismList object carrying a list of pairwise automorphisms between the DNA sequences from the MSA of primate somatic cytochrome C grouped by automorphism's coefficients. The grouping derives from the dataset brca1_autm after applying function automorphism_bycoef.
Usage
data("autby_coef", package = "GenomAutomorphism")Format
AutomorphismByCoefList class object.
Examples
## Load the data set
data("autby_coef", package = "GenomAutomorphism")
autby_coef
#> AutomorphismByCoefList object of length 190:
#> $human_1.human_2
#> AutomorphismByCoef object with 239 ranges and 7 metadata columns:
#> seqnames ranges strand | seq1 seq2 aa1
#> <Rle> <IRanges> <Rle> | <character> <character> <character>
#> [1] 1 1-238 + | ATG ATG M
#> [2] 1 1-238 + | GAT GAT D
#> [3] 1 1-238 + | TTA TTA L
#> [4] 1 1-238 + | TCT TCT S
#> [5] 1 1-238 + | GCT GCT A
#> ... ... ... ... . ... ... ...
#> [235] 1 511-761 + | CCC CCC P
#> [236] 1 511-761 + | CTT CTT L
#> [237] 1 511-761 + | CCT CCT P
#> [238] 1 511-761 + | ATA ATA I
#> [239] 1 511-761 + | TGA TGA *
#> aa2 autm mut_type cube
#> <character> <numeric> <character> <character>
#> [1] M 1 HHH ACGT
#> [2] D 1 HHH ACGT
#> [3] L 1 HHH ACGT
#> [4] S 1 HHH ACGT
#> [5] A 1 HHH ACGT
#> ... ... ... ... ...
#> [235] P 1 HHH ACGT
#> [236] L 1 HHH ACGT
#> [237] P 1 HHH ACGT
#> [238] I 1 HHH ACGT
#> [239] * 1 HHH ACGT
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
#>
#> ...
#> <189 more elements>
## Mutation type found in the data
unique(autby_coef$human_1.human_2$mut_type)
#> [1] "HHH" "HRH" "HYH" "YHH" "HHY" "RHH"