StructuredXStringSet: StructuredRNAStringSet for storing DotBracketAnnotation...

In FelixErnst/Structstrings: Implementation of the dot bracket annotations with Biostrings

StructuredRNAStringSet for storing DotBracketAnnotation alongside nucleotide sequences

Description

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.

Usage

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)

Arguments

x	For the Structured*StringSet constructors: Either a character vector, or an RNAString, RNAStringSet object. For writeStructuredXStringSet: A StructuredRNAStringSet derivative.
structure, value	A DotBracketStringSet
use.names, type, filepath, nrec, skip, seek.first.rec, append, ...	See DotBracketStringSet-io
compress	See getBasePairing or DotBracketStringSet-io
return.sequence	TRUE(default) or FALSE: Whether the sequence should be returned in the base column.
bracket.type	getLoopIndices: Which dot bracket annotation type should be converted into loop indices? Only usable, if more than one is present. (1L = '()', 2L = '<>', 3L = '[]', 4L = '{}')
warn.type.drops	See getLoopIndices

Details

the dotbracket function allows access to the included DotBracketStringSet.

Value

a StructuredRNAStringSet object.

Examples

str <- DotBracketStringSet("(())")
seq <- RNAStringSet("AGCU")
sdbs <- StructuredRNAStringSet(seq,str)

FelixErnst/Structstrings documentation built on March 26, 2024, 9:29 p.m.