getBasePairing converts a dot bracket annotation into a
data.frame. Base pairing is indicated by corresponding numbers
in the forward and reverse columns.
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a GRanges object created by
character vectors describing a nucleotide sequence
structure in the dot bracket annotations. Valid characters are:
optional: character vectors describing a nucleotide sequence. The same number of sequences with the same length as the dot bracket string have to be used. Each nucleotide sequence has to be a character vector. The identity of the nucleotides are not control, so in theory all letters can be used.
The result is a data.frame with following columns: pos, forward, reverse, chr
and base (if
sequence was provided or a
GRanges objects was
used). If a position is unpaired, forward and reverse will be
otherwise it will match the base paired positions.
return a list of list of loop ids.
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