gettRNABasePairing: Accessing Dot Bracket annotation of tRNAs
In tRNA: Analyzing tRNA sequences and structures

Description Usage Arguments Value Examples

gettRNABasePairing 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 signature 'GRanges'
gettRNABasePairing(x, with.nucleotides = FALSE)

## S4 method for signature 'GRanges'
gettRNALoopIDs(x)

`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`.
`with.nucleotides`	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.

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data("gr", package = "tRNA")
gettRNABasePairing(gr[1])
gettRNALoopIDs(gr[1])

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, basename, cbind, colnames,
    dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:base’:

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Structstrings
Loading required package: Biostrings
Loading required package: XVector

Attaching package: ‘Biostrings’

The following object is masked from ‘package:base’:

    strsplit

There were 50 or more warnings (use warnings() to see the first 50)
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           .

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