For the sake of saving memory, each
Automorphism-class
objects is stored in an AutomorphismList-class, which does
not inherits from a GRanges-class.
Usage
getAutomorphisms(x, ...)
# S4 method for AutomorphismList
getAutomorphisms(x)
# S4 method for list
getAutomorphisms(x)
# S4 method for DataFrame_OR_data.frame
getAutomorphisms(x)Value
This function returns an AutomorphismList-class
object as a list of Automorphism-class objects, which inherits
from GRanges-class objects.
Details
This function just transform each Automorphism-class
object into an object from the same class but now inheriting from a
GRanges-class.
Examples
## Load a dataset
data("autm", package = "GenomAutomorphism")
aut <- mcols(autm)
aut ## This a DataFrame object
#> DataFrame with 7100 rows and 8 columns
#> seq1 seq2 aa1 aa2 coord1 coord2
#> <character> <character> <character> <character> <numeric> <numeric>
#> 1 ATG ATG M M 50 50
#> 2 GAG GAG E E 10 10
#> 3 AGC AGC S S 33 33
#> 4 CTT CTT L L 55 55
#> 5 GTT GTC V V 59 57
#> ... ... ... ... ... ... ...
#> 7096 CTT CTT L L 55 55
#> 7097 GTT GTT V V 59 59
#> 7098 AAT AAC N N 3 1
#> 7099 AAC AAC N N 1 1
#> 7100 TAA TAA * * 12 12
#> autm cube
#> <numeric> <character>
#> 1 1 ACGT
#> 2 1 ACGT
#> 3 1 ACGT
#> 4 1 ACGT
#> 5 27 ACGT
#> ... ... ...
#> 7096 1 ACGT
#> 7097 1 ACGT
#> 7098 43 ACGT
#> 7099 1 ACGT
#> 7100 1 ACGT
## The natural ranges for the sequence (from 1 to length(aut)) are added
getAutomorphisms(aut)
#> Automorphism object with 7100 ranges and 8 metadata columns:
#> seqnames ranges strand | seq1 seq2 aa1
#> <Rle> <IRanges> <Rle> | <character> <character> <character>
#> [1] 1 1 + | ATG ATG M
#> [2] 1 2 + | GAG GAG E
#> [3] 1 3 + | AGC AGC S
#> [4] 1 4 + | CTT CTT L
#> [5] 1 5 + | GTT GTC V
#> ... ... ... ... . ... ... ...
#> [7096] 1 7096 + | CTT CTT L
#> [7097] 1 7097 + | GTT GTT V
#> [7098] 1 7098 + | AAT AAC N
#> [7099] 1 7099 + | AAC AAC N
#> [7100] 1 7100 + | TAA TAA *
#> aa2 coord1 coord2 autm cube
#> <character> <numeric> <numeric> <numeric> <character>
#> [1] M 50 50 1 ACGT
#> [2] E 10 10 1 ACGT
#> [3] S 33 33 1 ACGT
#> [4] L 55 55 1 ACGT
#> [5] V 59 57 27 ACGT
#> ... ... ... ... ... ...
#> [7096] L 55 55 1 ACGT
#> [7097] V 59 59 1 ACGT
#> [7098] N 3 1 43 ACGT
#> [7099] N 1 1 1 ACGT
#> [7100] * 12 12 1 ACGT
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
## A list of automorphisms
aut <- list(aut, aut)
getAutomorphisms(aut)
#> AutomorphismList object of length: 2
#> names(0):
#> -------
#> Automorphism object with 7100 ranges and 8 metadata columns:
#> seqnames ranges strand | seq1 seq2 aa1
#> <Rle> <IRanges> <Rle> | <character> <character> <character>
#> [1] 1 1 + | ATG ATG M
#> [2] 1 2 + | GAG GAG E
#> [3] 1 3 + | AGC AGC S
#> [4] 1 4 + | CTT CTT L
#> [5] 1 5 + | GTT GTC V
#> ... ... ... ... . ... ... ...
#> [7096] 1 7096 + | CTT CTT L
#> [7097] 1 7097 + | GTT GTT V
#> [7098] 1 7098 + | AAT AAC N
#> [7099] 1 7099 + | AAC AAC N
#> [7100] 1 7100 + | TAA TAA *
#> aa2 coord1 coord2 autm cube
#> <character> <numeric> <numeric> <numeric> <character>
#> [1] M 50 50 1 ACGT
#> [2] E 10 10 1 ACGT
#> [3] S 33 33 1 ACGT
#> [4] L 55 55 1 ACGT
#> [5] V 59 57 27 ACGT
#> ... ... ... ... ... ...
#> [7096] L 55 55 1 ACGT
#> [7097] V 59 59 1 ACGT
#> [7098] N 3 1 43 ACGT
#> [7099] N 1 1 1 ACGT
#> [7100] * 12 12 1 ACGT
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
#> ...
#> <-1 more Automorphism element(s)>
#> Two slots: 'DataList' & 'SeqRanges'
#> -------
## Automorphism-class inherits from 'GRanges-class'
aut <- as(autm, "GRanges")
as(aut, "Automorphism")
#> Automorphism object with 7100 ranges and 8 metadata columns:
#> seqnames ranges strand | seq1 seq2 aa1
#> <Rle> <IRanges> <Rle> | <character> <character> <character>
#> [1] 1 1 + | ATG ATG M
#> [2] 1 2 + | GAG GAG E
#> [3] 1 3 + | AGC AGC S
#> [4] 1 4 + | CTT CTT L
#> [5] 1 5 + | GTT GTC V
#> ... ... ... ... . ... ... ...
#> [7096] 1 7096 + | CTT CTT L
#> [7097] 1 7097 + | GTT GTT V
#> [7098] 1 7098 + | AAT AAC N
#> [7099] 1 7099 + | AAC AAC N
#> [7100] 1 7100 + | TAA TAA *
#> aa2 coord1 coord2 autm cube
#> <character> <numeric> <numeric> <numeric> <character>
#> [1] M 50 50 1 ACGT
#> [2] E 10 10 1 ACGT
#> [3] S 33 33 1 ACGT
#> [4] L 55 55 1 ACGT
#> [5] V 59 57 27 ACGT
#> ... ... ... ... ... ...
#> [7096] L 55 55 1 ACGT
#> [7097] V 59 59 1 ACGT
#> [7098] N 3 1 43 ACGT
#> [7099] N 1 1 1 ACGT
#> [7100] * 12 12 1 ACGT
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths