gettRNABasePairing {tRNA} | R Documentation |
getBasePairing
converts a dot bracket annotation into a
data.frame
. Base pairing is indicated by corresponding numbers
in the forward and reverse columns.
gettRNABasePairing(x) gettRNALoopIDs(x) ## S4 method for signature 'GRanges' gettRNABasePairing(x) getBasePairing(dotBracket, sequence) ## S4 method for signature 'GRanges' gettRNALoopIDs(x) getLoopIDs(dotBracket)
x |
a GRanges object created by |
dotBracket |
character vectors describing a nucleotide sequence
structure in the dot bracket annotations. Valid characters are:
|
sequence |
optional: character vectors describing a nucleotide sequence. The same number of sequences with the same length as the dot bracket string have to be used. Each nucleotide sequence has to be a character vector. The identity of the nucleotides are not control, so in theory all letters can be used. |
getBasePairing
:
The result is a data.frame with following columns: pos, forward, reverse, chr
and base (if sequence
was provided or a GRanges
objects was
used). If a position is unpaired, forward and reverse will be 0
,
otherwise it will match the base paired positions.
gettRNALoopIDs
, getLoopIDs
:
return a list of list of loop ids.
data("gr", package = "tRNA", envir = environment()) gettRNABasePairing(gr[1]) getBasePairing(gr[1]$tRNA_str) gettRNALoopIDs(gr[1]) getLoopIDs(gr[1]$tRNA_str)