findPairedBases: Determines paired bases from secondary structure string

In ncRNAtools: An R toolkit for non-coding RNA

Description

Determines bases that form pairs in a given RNA sequence from the secondary structure string of the RNA sequence.

Usage

findPairedBases(secondaryStructureString, sequence)

Arguments

secondaryStructureString	A string representing the secondary structure of the RNA sequence in the Dot-Bracket format.
sequence	string with the RNA sequence corresponding to the provided secondary structure string. Should contain only standard RNA symbols (i.e., "A", "U", "G" and "C").

Value

A dataframe where each row denotes a base pair. The dataframe comprises the following 4 columns:

Position1	position in the sequence of the nucleotide involved in the base pair closest to the 5' end of the RNA.
Position2	position in the sequence of the nucleotide involved in the base pair closest to the 3' end of the RNA.
Nucleotide1	nucleotide type of the base in Position1.
Nucleotide2	nucleotide type of the base in Position2.

Examples

# Read a Dot Bracket file with the secondary structure of an RNA sequence:

exampleDotBracketFile <- system.file("extdata", "exampleDotBracket.dot", 
                                     package="ncRNAtools")

exampleDotBracket <- readDotBracket(exampleDotBracketFile)

# Generate a dataframe of paired bases from the returned secondary structure
# string:

pairedBasesTable <- findPairedBases(secondaryStructureString=exampleDotBracket$secondaryStructure,
sequence=exampleDotBracket$sequence)

ncRNAtools documentation built on Nov. 8, 2020, 8:14 p.m.