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Index representing the evolutionary distance between two genomes.

Source: R/K80_distance.R
K80_distance.Rd

The K80 distance is calculated as -0.5 * log((1 - 2 * p - q) * sqrt(1 - 2 * q)). See WIKI for more details.

Usage

K80_distance(train_parameters)

Arguments

train_parameters

A list containing the probabilities of the alignment.

Value

Returns a numeric value show the evolutionary distance between two genomes. the larger the value, the more different the two genomes are.ss

Note

Here, the probability ranges from 0 to 1. The list input can contain other information, but the function will only use the name in this format probability_REF_ALT

See also

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

Examples

parameters <- readTrainFile(system.file("extdata/example.train", package = "GenomicBreaks"))
K80_distance(parameters)
#> [1] 0.01616738