R/AllGenerics.R, R/tRNA-dotbracket.R
gettRNABasePairing.RdgettRNABasePairing converts the dot bracket annotation into a
DotBracketDataFrame. Base pairing is indicated by cosrresponding
numbers in the forward and reverse columns. For more detail have a look at
getBasePairing.
gettRNALoopIDs converts the dot bracket annotation into a
LoopIDList. For more details have a look at
getLoopIDList.
gettRNABasePairing(x, with.nucleotides = FALSE)
gettRNALoopIDs(x)
# S4 method for GRanges
gettRNABasePairing(x, with.nucleotides = FALSE)
# S4 method for GRanges
gettRNALoopIDs(x)a GRanges object created by import.tRNAscanAsGRanges or
GRanges with equivalent information. The tRNA_str and tRNA_seq
columns will be used to construct a StructuredXStringSet and used for input
into getBasePairing.
a single logical value: should the nucleotides be saved alongside the base pairing information in the 'base' column?
gettRNABasePairing:
The result is a DotBracketDataFrame with following columns: pos,
forward, reverse, character and base. If a position is unpaired, forward and
reverse will be 0, otherwise it will match the base paired positions.
gettRNALoopIDs: return a list of list of loop ids.
data("gr", package = "tRNA")
gettRNABasePairing(gr[1])
#> SplitDotBracketDataFrameList of length 1
#> [[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 .
#>
gettRNALoopIDs(gr[1])
#> LoopIndexList of length 1
#> [[""]] 1 2 3 4 5 5 6 6 6 7 8 9 9 9 9 9 ... 19 19 19 18 17 16 15 6 5 5 4 3 2 1 0