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DotBracketDataFrame() DBDF() DotBracketDataFrameList() DBDFL() SplitDotBracketDataFrameList() SDBDFL()
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DataFrame for storing base pairing information |
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DotBracketString() DB() DotBracketStringSet() DBS() DotBracketStringSetList() DBSL() alphabet(<DotBracketString>) encoding(<DotBracketString>)
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The DotBracketString, DotBracketStringSet and DotBracketStringSetList classes |
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readDotBracketStringSet() writeDotBracketStringSet() saveDotBracketStringSet()
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Reading and writing DotBracketStringSet objects |
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LoopIndexList()
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LoopIndexList: base pairing information as a list of integer values |
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dbs nseq
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Structstrings example data |
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DOTBRACKET_CHAR_VALUES DOTBRACKET_ALPHABET STRUCTURE_NEUTRAL_CHR STRUCTURE_OPEN_CHR STRUCTURE_CLOSE_CHR `[<-`(<DotBracketDataFrame>) `colnames<-`(<CompressedSplitDotBracketDataFrameList>) seqtype(<DotBracketString>) subseq(<DotBracketString>) `subseq<-`(<DotBracketString>) `subseq<-`(<DotBracketStringSet>)
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Structstrings internals |
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Structstrings
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Structstrings: implementation of the dot bracket annotations with Biostrings |
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StructuredRNAStringSet() dotbracket() `dotbracket<-`() readStructuredRNAStringSet() writeStructuredXStringSet() getBasePairing(<StructuredXStringSet>) getLoopIndices(<StructuredXStringSet>)
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StructuredRNAStringSet for storing DotBracketAnnotation alongside nucleotide sequences |
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convertAnnotation()
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Convert between dot bracket annotations |
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getBasePairing() getDotBracket() getLoopIndices()
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Accessing Dot Bracket annotation |