Several methods are available to be applied on
Automorphism-class and AutomorphismList-class
objects.
Usage
as.AutomorphismList(x, grs = GRanges(), ...)
# S4 method for GRangesList,GRanges_OR_NULL
as.AutomorphismList(x, grs = GRanges(), ...)
# S4 method for list,GRanges_OR_NULL
as.AutomorphismList(x, grs = GRanges(), ...)Arguments
- x
A
DataFrameor aautomorphismsclass object.- grs
A
GRanges-classobject.- ...
Not in use yet.
Examples
## Load a dataset
data("brca1_autm", package = "GenomAutomorphism")
## Let's transforming into a list of Automorphisms-class objects
x1 <- as.list(brca1_autm[seq(2)])
## Now, object 'x1' is transformed into a AutomorphismList-class object
as.AutomorphismList(x1)
#> AutomorphismList object of length: 2
#> names(2): human_1.human_2 human_1.gorilla_1
#> -------
#> Automorphism object with 761 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 + | GAT GAT D
#> [3] 1 3 + | TTA TTA L
#> [4] 1 4 + | TCT TCT S
#> [5] 1 5 + | GCT GCT A
#> ... ... ... ... . ... ... ...
#> [757] 1 757 + | CAC CAC H
#> [758] 1 758 + | AGC AGC S
#> [759] 1 759 + | CAC CAC H
#> [760] 1 760 + | TAC TAC Y
#> [761] 1 761 + | TGA TGA *
#> aa2 coord1 coord2 autm cube
#> <character> <numeric> <numeric> <numeric> <character>
#> [1] M 50 50 1 ACGT
#> [2] D 11 11 1 ACGT
#> [3] L 60 60 1 ACGT
#> [4] S 31 31 1 ACGT
#> [5] A 27 27 1 ACGT
#> ... ... ... ... ... ...
#> [757] H 5 5 1 ACGT
#> [758] S 33 33 1 ACGT
#> [759] H 5 5 1 ACGT
#> [760] Y 13 13 1 ACGT
#> [761] * 44 44 1 ACGT
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
#> ...
#> <1 more DFrame element(s)>
#> Two slots: 'DataList' & 'SeqRanges'
#> -------
## Alternatively, let's transform the list 'x1' into a GRangesList-class
## object.
x1 <- GRangesList(x1)
## Next, object 'x1' is transformed into a AutomorphismList-class object
as.AutomorphismList(x1)
#> AutomorphismList object of length: 2
#> names(2): human_1.human_2 human_1.gorilla_1
#> -------
#> Automorphism object with 761 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 + | GAT GAT D
#> [3] 1 3 + | TTA TTA L
#> [4] 1 4 + | TCT TCT S
#> [5] 1 5 + | GCT GCT A
#> ... ... ... ... . ... ... ...
#> [757] 1 757 + | CAC CAC H
#> [758] 1 758 + | AGC AGC S
#> [759] 1 759 + | CAC CAC H
#> [760] 1 760 + | TAC TAC Y
#> [761] 1 761 + | TGA TGA *
#> aa2 coord1 coord2 autm cube
#> <character> <numeric> <numeric> <numeric> <character>
#> [1] M 50 50 1 ACGT
#> [2] D 11 11 1 ACGT
#> [3] L 60 60 1 ACGT
#> [4] S 31 31 1 ACGT
#> [5] A 27 27 1 ACGT
#> ... ... ... ... ... ...
#> [757] H 5 5 1 ACGT
#> [758] S 33 33 1 ACGT
#> [759] H 5 5 1 ACGT
#> [760] Y 13 13 1 ACGT
#> [761] * 44 44 1 ACGT
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
#> ...
#> <1 more DFrame element(s)>
#> Two slots: 'DataList' & 'SeqRanges'
#> -------