Pick multiple de-replication sets from a pangenome, uses furrr::future_map Be sure to set your 'plan()'!!!

Usage

pick_derep_sets(pan_PA, num_sets = 25, desired_coverage = 0.95)

Arguments

pan_PA: A pangenome gene presence/absence matrix, genomes as columns, genes as rows
num_sets: The number of sets to select (25)
desired_coverage: the proportion of genes in the pangenome to cover (.95)

Value

a tibble with two columns:

the random seeds used,
list column containing the dereplication sets

Examples

sets <- pick_derep_sets(example_pangenome_matrix)
sets$selection_set[[1]]
#> [[1]]
#> [1] "genome_4"  "genome_85" "genome_19" "genome_55" "genome_52"
#> 
#> [[2]]
#> [1] 771 863 909 943 964
#> 
#> [[3]]
#> [1] 0.771 0.863 0.909 0.943 0.964
#> 
sets$selection_set[[10]]
#> [[1]]
#> [1] "genome_29" "genome_20" "genome_31" "genome_11" "genome_58"
#> 
#> [[2]]
#> [1] 768 867 910 940 961
#> 
#> [[3]]
#> [1] 0.768 0.867 0.910 0.940 0.961
#>