count_gene_families_by_sentinel_site — count_gene_families_by_sentinel

A function to count gene families by sentinel_site

count_gene_families_by_sentinel_site(
  long_acquired_gene_amr_data,
  subclass_counts_by_sentinel_site,
  drug_subclasses = NULL
)

Arguments

long_acquired_gene_amr_data	The acquired AMR data as obtained by the pivot_metadata_to_long_amr function
subclass_counts_by_sentinel_site	Counts of each subclass by sentinel_site as obtained by the count_AMR_subclasses_by_sentinel_site function
drug_subclasses	The desired drug subclasses to count (specifying none will count all but this may not be desired)

Value

gene_family_counts_by_sentinel_site Counts of each gene per subclass by sentinel_site

# A tibble: 6 x 5
Sentinel Site subclass gene_family count proportion
<chr> <fct> <fct> <int> <dbl>
1 UCH BETA-LACTAM blaI 1 0.00246
2 UCH BETA-LACTAM blaLAP 2 0.00493
3 UCH BETA-LACTAM blaOXA 11 0.0271
4 UCH BETA-LACTAM blaPSE 16 0.0394
5 UCH BETA-LACTAM blaSHV 363 0.894
6 UCH BETA-LACTAM blaTEM 161 0.397