Index representing how the karyotype changes between chromosomes of two genomes

The index is calculated as the mean of the number of chromosomes in the two genomes. ###############

Usage

karyotype_index(gb)

Arguments

gb

A GBreaks object.

Value

Returns a numeric value between 0 and 1. 0 is expected for same karyotype genomes.

Note

Here, the definition of ‘karyotype change’ is 1 - (the mean value of change score for each chromosome in the reference genome. The change score for chromosome Ref is calculated as 1 / (number of mapped chromosomes in the query genome). To be noticed, the mapped length of mapped chromosome in the query genome should be at least 10% of the length of the reference chromosome. if chromosome Ref has only one mapped chromosome in the query genome, the change score is 1. For 2 chromosomes, the change score is 0.5. For the symmetry, the sum of change scores for each chromosome in query will be normalized to 1 if the sum is more than 1.

See also

Other Similarity indexes: GOC(), JC69_distance(), K80_distance(), T92_distance(), correlation_index(), readTrainFile(), strand_randomisation_index(), synteny_index()

Examples

gb       <- GRanges(c("Ref:100-200:+",   "Ref:400-500:+",    "Re2:600-700:+"))
gb$query <- GRanges(c("Que:1100-1200:+", "Que2:1700-1800:+", "Que2:1500-1600:+"))
karyotype_index(gb)
#> [1] 0.5