Breakpoint graph properties

Computes the breakpoint graph of a pair of chromosomes and returns key properties of the graph, which are used in various rearrangement estimates.

Usage

breakpointGraphProperties(gb)

Arguments

gb

A GBreaks object.

Value

A list containing the following properties of the breakpoint graph: 1. N : the total number of places where a breakpoint could occur (which is the same as the number_aligned_blocks + 1); 2. nbBreakpoints : the total number of breakpoints in the extended permutation; 3. nbCycles : the total number of cycles in the breakpoint graph (trivial and non-trivial cycles).

References

Hannenhalli, Sridhar, and Pavel A. Pevzner. "Transforming cabbage into turnip: polynomial algorithm for sorting signed permutations by reversals." Journal of the ACM (JACM) 46.1 (1999): 1-27.

See also

Other Breakpoint graph functions: bp_count(), breakpoint_graph(), components_graph(), cycle_count(), cycle_nontrivial_count(), extendedPermutation(), hurdles_count(), is_fortress(), is_interleaving(), superhurdles_count()

Other Rearrangement distances: inversionDistance(), inversionEstimate_BD()

Other Similarity indexes: F81_distance(), GOC(), HKY85_distance(), JC69_distance(), JC69_distance_allseq(), K80_distance(), K80_gap_distance(), P_distance(), T92_distance(), TN93_distance(), correlation_index(), inversionDistance(), inversionEstimate_BD(), karyotype_index(), logDet_distance(), slidingWindow(), strand_randomisation_index(), synteny_index(), tau_index()

Author

Priscila Biller

Examples

breakpointGraphProperties(exampleInversionHP1999fig4a)
#> $N
#> [1] 9
#> 
#> $nbBreakpoints
#> [1] 9
#> 
#> $nb_cycles
#> [1] 3
#>