A class definition to store conserved gene/genomic regions found in a MSA.
Source:R/allClasses.R
AutomorphismByCoef.RdObjects from this class are generated by function
automorphism_bycoef.
AutomorphismByCoefList-class methods
Examples
## Let's transform a AutomorphismByCoefList-class object into an
## AutomorphismByCoef-class object
data("autby_coef")
unlist(autby_coef[1:2])
#> AutomorphismByCoef object with 683 ranges and 7 metadata columns:
#> seqnames ranges strand | seq1 seq2
#> <Rle> <IRanges> <Rle> | <character> <character>
#> human_1.human_2 1 1-238 + | ATG ATG
#> human_1.human_2 1 1-238 + | GAT GAT
#> human_1.human_2 1 1-238 + | TTA TTA
#> human_1.human_2 1 1-238 + | TCT TCT
#> human_1.human_2 1 1-238 + | GCT GCT
#> ... ... ... ... . ... ...
#> human_1.gorilla_1 1 729-761 + | CCC CCC
#> human_1.gorilla_1 1 729-761 + | ATC ATC
#> human_1.gorilla_1 1 729-761 + | CAC CAC
#> human_1.gorilla_1 1 729-761 + | AGC AGC
#> human_1.gorilla_1 1 729-761 + | TGA TGA
#> aa1 aa2 autm mut_type cube
#> <character> <character> <numeric> <character> <character>
#> human_1.human_2 M M 1 HHH ACGT
#> human_1.human_2 D D 1 HHH ACGT
#> human_1.human_2 L L 1 HHH ACGT
#> human_1.human_2 S S 1 HHH ACGT
#> human_1.human_2 A A 1 HHH ACGT
#> ... ... ... ... ... ...
#> human_1.gorilla_1 P P 1 HHH ACGT
#> human_1.gorilla_1 I I 1 HHH ACGT
#> human_1.gorilla_1 H H 1 HHH ACGT
#> human_1.gorilla_1 S S 1 HHH ACGT
#> human_1.gorilla_1 * * 1 HHH ACGT
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
## Herein a 'list' object of AutomorphismByCoef-class objects
lista <- list(human = autby_coef[[1]], gorilla = autby_coef[[2]])
## Let's transform the the last list 'lista' into an
## AutomorphismByCoefList-class object
aut <- as(lista, "AutomorphismByCoefList")
aut
#> AutomorphismByCoefList object of length 2:
#> $human
#> 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
#>
#> $gorilla
#> AutomorphismByCoef object with 444 ranges and 7 metadata columns:
#> seqnames ranges strand | seq1 seq2 aa1
#> <Rle> <IRanges> <Rle> | <character> <character> <character>
#> [1] 1 1-59 + | ATG ATG M
#> [2] 1 1-59 + | GAT GAT D
#> [3] 1 1-59 + | TTA TTA L
#> [4] 1 1-59 + | TCT TCT S
#> [5] 1 1-59 + | GCT GCT A
#> ... ... ... ... . ... ... ...
#> [440] 1 729-761 + | CCC CCC P
#> [441] 1 729-761 + | ATC ATC I
#> [442] 1 729-761 + | CAC CAC H
#> [443] 1 729-761 + | AGC AGC S
#> [444] 1 729-761 + | 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
#> ... ... ... ... ...
#> [440] P 1 HHH ACGT
#> [441] I 1 HHH ACGT
#> [442] H 1 HHH ACGT
#> [443] S 1 HHH ACGT
#> [444] * 1 HHH ACGT
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
#>
## Let's get the element names from object 'aut'
names(aut)
#> [1] "human" "gorilla"
## Let's assign new names
names(aut) <- c("human_1", "gorilla_1")
names(aut)
#> [1] "human_1" "gorilla_1"