Computes the minimal number of inversions required to sort a signed permutation using the Hannenhalli and Pevzner algorithm.
Arguments
- gb
A GBreaks object containing genome data from which a permutation vector can be extracted using the
permutationVector()function.
Details
This function uses several internal helper functions (e.g., extendedPermutation,
breakpoint_graph, hurdles_count, superhurdles_count, and others) to
compute properties of the breakpoint graph and identify cycles, hurdles and superhurdles.
It also depends on permutationVector(), which is defined in another .R file.
This algorithm was designed to work in a single, linear chromosome alignment. Although the function still works if the GBreaks object involves more than one chromosome, the returned value for the minimal number of inversions will imply in non-usual inversions if different chromosomes have orthologous regions.
See also
permutationVector for generating the permutation vector.