R/AllGenerics.R, R/tRNA-sequences.R, R/tRNA-structures.R
gettRNAstructureSeqs.RdgettRNAstructureGRanges returns a list of GRanges describing the
boundaries of tRNA structures as extracted from the dot bracket annotation.
The dot bracket annotation is parsed using gettRNABasePairing, which
internally uses getBasePairing.
gettRNAstructureSeq returns split or partial tRNA sequences based on
the structure information. Variations in the ength of structure features can
be padded to retrieve sequences of equal length. If sequences are joined by
setting joinCompletely = FALSE, the boundaries of the tRNA structure
are stored in the result as metadata. They can be accessesed as an IRanges
object by using metadata(seq)[["tRNA_structures"]].
gettRNAstructureGRanges(x, structure = "")
gettRNAstructureSeqs(
x,
structure = "",
joinCompletely = FALSE,
joinFeatures = FALSE,
padSequences = TRUE
)
# S4 method for GRanges
gettRNAstructureSeqs(
x,
structure = "",
joinCompletely = FALSE,
joinFeatures = FALSE,
padSequences = TRUE
)
# S4 method for GRanges
gettRNAstructureGRanges(x, structure = "")a GRanges object with tRNA information. It has to pass the
istRNAGRanges function.
optional parameter for returning just partial sequences.
The following values are accepted:
anticodonStem, Dprime5, DStem, Dloop,
Dprime3, acceptorStem, anticodonloop,
variableLoop, TStem, Tloop, discriminator.
(default: structure = "")
Should the sequence parts, which are to be returned, be
joined into one sequence? (default: joinCompletely = FALSE))
Setting this to TRUE excludes joinFeatures be set to TRUE as well. In
addition, joinCompletely = TRUE uses automatically all sequence
structures.
Should the sequence parts, which are to be returned and
are from the same structure type, be joined into one sequence?
(default: joinCompletely = FALSE)) Setting this to TRUE excludes
joinCompletely be set to TRUE as well. joinCompletely takes
precedence.
parameter whether sequences of the same type
should be returned with the same length. For stems missing positions will be
filled up in the middle, for loops at the ends.
(default: padSequences = TRUE). If joinCompletely == TRUE this
is set to TRUE automatically.
a list of GRanges or DNAStringSet objects. In case
joinCompletly is set to TRUE a single DNAStringSet is returned.
data("gr", package = "tRNA")
gettRNAstructureGRanges(gr, structure = "anticodonLoop")
#> $anticodonLoop
#> IRanges object with 299 ranges and 0 metadata columns:
#> start end width
#> <integer> <integer> <integer>
#> TGG 31 37 7
#> TGC 32 38 7
#> CAA 31 37 7
#> AGA 31 37 7
#> TAA 31 37 7
#> ... ... ... ...
#> CAT 32 38 7
#> GAA 31 37 7
#> TTA 31 37 7
#> TAC 32 38 7
#> CAT 32 38 7
#>
gettRNAstructureSeqs(gr, structure = "anticodonLoop")
#> $anticodonLoop
#> RNAStringSet object of length 299:
#> width seq names
#> [1] 7 UUUGGGU TGG
#> [2] 7 CUUGCAA TGC
#> [3] 7 UUCAAGC CAA
#> [4] 7 UUAGAAA AGA
#> [5] 7 CUUAAGA TAA
#> ... ... ...
#> [295] 7 CUCAUAA CAT
#> [296] 7 UUGAAGA GAA
#> [297] 7 UUUUAGU TTA
#> [298] 7 UUUACAC TAC
#> [299] 7 GUCAUGA CAT
#>
gettRNABasePairing(gr[1:10])
#> SplitDotBracketDataFrameList of length 10
#> [[1]]
#> DotBracketDataFrame with 71 rows and 4 columns
#> pos forward reverse character
#> <integer> <integer> <integer> <character>
#> 1 1 1 70 <
#> 2 2 2 69 <
#> 3 3 3 68 <
#> 4 4 4 67 <
#> 5 5 5 66 <
#> ... ... ... ... ...
#> 67 67 67 4 >
#> 68 68 68 3 >
#> 69 69 69 2 >
#> 70 70 70 1 >
#> 71 71 0 0 .
#>
#> ...
#> <9 more elements>