Calculate genome 'novelty' from a list of selection sets returned by pick_derep_sets
Source:R/pangenome_tools.R
calculate_novelty.RdCalculate genome 'novelty' from a list of selection sets returned by pick_derep_sets
Value
a dataframe with the novelty scores of all genomes in the list 'Novelty' score for each genome is (number of selections) / median rank of selection
Examples
sets <- pick_derep_sets(example_pangenome_matrix)
genome_novelty <- calculate_novelty(sets)
genome_novelty
#> # A tibble: 26 × 8
#> asm_acc median_rank number_selections best_rank worst_rank novelty_score
#> <chr> <dbl> <int> <int> <int> <dbl>
#> 1 genome_55 2 15 2 4 7.5
#> 2 genome_19 3 10 3 4 3.33
#> 3 genome_31 2.5 8 2 4 3.2
#> 4 genome_72 3.5 6 2 5 1.71
#> 5 genome_11 3 5 2 5 1.67
#> 6 genome_8 2 3 2 4 1.5
#> 7 genome_85 4 5 2 5 1.25
#> 8 genome_20 3 3 2 5 1
#> 9 genome_28 3 3 3 3 1
#> 10 genome_60 4.5 4 3 5 0.889
#> # ℹ 16 more rows
#> # ℹ 2 more variables: log_novelty <dbl>, RANK <int>