readDotBracket: Reads a file with the sequence and secondary structure of an...
In LaraSellesVidal/ncRNAtools: An R toolkit for non-coding RNA

Description Usage Arguments Value References Examples

View source: R/ncRNAtools_readWriteFunctions.R

Reads a file with the secondary structure of an RNA in the CT format (Connectivity Table).

1	readDotBracket(filename)

filename

A string indicating the path to the Dot-Bracket file to be read. A description of the Dot-Bracket format can be found at https://www.tbi.univie.ac.at/RNA/ViennaRNA/doc/html/rna_structure_notations.html. Both basic and extended Dot-Bracket notations are accepted. The Dot-Bracket file should always contain at least two lines: the first one with the RNA sequence, and the second one with the secondary structure representation. The free energy of the secondary structure can be optionally present at the end of the secondary structure line, in kcal/mol. An additional optional line can precede these two, containing ">" as its first character followed by the name or description of the sequence.

A list with the following 4 elements:

`sequenceName`	name of the RNA sequence. Will be set to NA if no string starting with ">" is present at the beginning of the Dot-Bracket file
`sequence`	RNA sequence
`secondaryStructure`	string representing the secondary structure of the RNA in the Dot-Bracket format
`freeEnergy`	free energy of the secondary structure of the RNA, usually in kcal/mol. If not present in the Dot-Bracket file, it will be set to NA

https://software.broadinstitute.org/software/igv/RNAsecStructure

http://projects.binf.ku.dk/pgardner/bralibase/RNAformats.html

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

exampleDotBracket <- readDotBracket(exampleDotBracketFile)

# Since the file does not contain an initial line with the name of the sequence,
# sequenceName is set to NA