Index representing how the karyotype changes between chromosomes of two genomes

This function is used to read the train file from LAST and extract the final parameters.

Usage

readTrainFile(input_file)

Arguments

input_file

A string of the path to the train file from LAST.

Value

Returns a list of parameters from LAST train file. "PercentSimilarity", "PercentSimilarityNogaps", "mean_delete_size", "mean_insert_size", "substitution_percent_identity", "probability", "matchProb", "delOpenProb", "insOpenProb", "delExtendProb", "insExtendProb", "endProb"

See also

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

Examples

parameters <- readTrainFile(system.file("extdata/example.train", package = "GenomicBreaks"))
parameters
#> $mean_delete_size
#> [1] 6.25287
#> 
#> $mean_insert_size
#> [1] 6.80408
#> 
#> $substitution_percent_identity
#> [1] 98.4025
#> 
#> $probability_A_A
#> [1] 0.289718
#> 
#> $probability_A_C
#> [1] 0.000727394
#> 
#> $probability_A_G
#> [1] 0.00253215
#> 
#> $probability_A_T
#> [1] 0.000611873
#> 
#> $probability_C_A
#> [1] 0.000689766
#> 
#> $probability_C_C
#> [1] 0.202294
#> 
#> $probability_C_G
#> [1] 0.000810395
#> 
#> $probability_C_T
#> [1] 0.00261617
#> 
#> $probability_G_A
#> [1] 0.00261617
#> 
#> $probability_G_C
#> [1] 0.000810395
#> 
#> $probability_G_G
#> [1] 0.202294
#> 
#> $probability_G_T
#> [1] 0.000689766
#> 
#> $probability_T_A
#> [1] 0.000611873
#> 
#> $probability_T_C
#> [1] 0.00253215
#> 
#> $probability_T_G
#> [1] 0.000727394
#> 
#> $probability_T_T
#> [1] 0.289718
#> 
#> $matchProb
#> [1] 0.997811
#> 
#> $delOpenProb
#> [1] 0.000895537
#> 
#> $insOpenProb
#> [1] 0.000766701
#> 
#> $delExtendProb
#> [1] 0.795939
#> 
#> $insExtendProb
#> [1] 0.795939
#> 
#> $endProb
#> [1] 0.999737
#>