Functions to compute covariation, percent identity conservation, and percent canonical basepairs given a multiple sequence alignment and optionally a secondary structure. Statistics can be computed for a single base, basepair, helix or entire alignment.
Functions to coerce a structure into a helix data frame, and to check whether a structure is a valid helix data frame. A helix data frame is a data frame, so any structure coercible into a data.frame can become a helix data frame.
Calculates the frequency of each basepair in a given helix structure. Internally, breaks helices into basepairs, and returns a structure of unique basepairs, where the values is its frequency, regardless of original value.
Functions to generate colours for helices by various rules, including integer counts, value ranges, percent identity covariation, conservation, percentage canonical basepair, basepair frequency, and non-pseudoknotted groups.
● Data Source:
BioConductor
● Keywords: color
● Alias: colourByBasepairFrequency, colourByCanonical, colourByConservation, colourByCount, colourByCovariation, colourByUnknottedGroups, colourByValue, defaultPalette
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Given a helix data frame, expands a helix of arbitrary length into helices of length 1 (i.e. basepairs). Also does the reverse operation of clustering consecutive basepairs (or helices), and merging/collapsing them into a single helix.
Given a helix data frame, checks if helices are conflicting, duplicating, or overlapping, and returns an array of numeric values, where 0 is FALSE and 1 is TRUE. Values in between 0 and 1 occur when a single helix has multiple basepairs with different values, the number observed in this case is the mean of the basepair values within the helix. See details for exact definition of the three types of events.
Given a multiple sequence alignment and a corresponding secondary structure, nucleotides in the sequence alignment will be coloured according to the basepairing and conservation status, where green is the most commonly observed valid basepair in the column, dark blue being valid covariation (i.e. mutation into another valid basepair), cyan is one-sided mutation that retains the basepair, and red is a mutation where the basepair has been lost.
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