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Index representing the evolutionary distance between two genomes.

Source: R/T92_distance.R
T92_distance.Rd

The T92 distance is calculated as -h * log(1 - p / h - q) - 0.5 * (1 - h) * log(1 - 2 * q). See WIKI for more details.

Usage

T92_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.

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(), K80_distance(), correlation_index(), karyotype_index(), readTrainFile(), strand_randomisation_index(), synteny_index()

Examples

parameters <- readTrainFile(system.file("extdata/example.train", package = "GenomicBreaks"))
T92_distance(parameters)
#> [1] 0.01617185