Description Usage Arguments Details Value Examples
View source: R/Structstrings-StructuredXStringSet.R
The StructuredXStringSet
class can be used to store structure
information alongside RNA sequences. The class behaves like the
QualityScaledXStringSet
classes.
Please note, that this does not check for validity regarding base pairing capabilities.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 | StructuredRNAStringSet(x, structure)
dotbracket(x)
dotbracket(x) <- value
## S4 method for signature 'StructuredXStringSet'
dotbracket(x)
## S4 replacement method for signature 'StructuredXStringSet'
dotbracket(x) <- value
readStructuredRNAStringSet(
filepath,
nrec = -1L,
skip = 0L,
seek.first.rec = FALSE,
use.names = TRUE
)
writeStructuredXStringSet(x, filepath, append = FALSE, compress = FALSE, ...)
## S4 method for signature 'StructuredXStringSet'
getBasePairing(x, compress = TRUE, return.sequence = FALSE)
## S4 method for signature 'StructuredXStringSet'
getLoopIndices(x, bracket.type, warn.type.drops = TRUE)
|
x |
For the |
structure, value |
A |
use.names, type, filepath, nrec, skip, seek.first.rec, append, ... |
See |
compress |
See |
return.sequence |
|
bracket.type |
|
warn.type.drops |
See |
the dotbracket
function allows access to the included
DotBracketStringSet
.
a StructuredRNAStringSet
object.
1 2 3 | str <- DotBracketStringSet("(())")
seq <- RNAStringSet("AGCU")
sdbs <- StructuredRNAStringSet(seq,str)
|
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