NA at the aggregate_counts step

Aggregate counts seems to generate an artefact (NA). I have all the categories defined in F3M_module_db but a counts for 'NA' is also generated. I checked in cereals_ref_db but there is no NA, same in all_sample_counts. The results is the same regardless taxonomic or functional agregation level.

Code :

Build the reference database

cereals_ref_db <- build_ref_db( funct_annotations_path = funct_annotations_path, gtdb_classification_path = gtdb_classification_path )

IMPORT MULTIPLE SAMPLES -------------------------------------------------

Path to the folder containing multiple sample files

folder_path <- "~/Documents/1 - PhD DOMINO/1 - WP4 - Microbial consortia/2 - Aliments fermentés traditionnels/f3m/add_functions_and_species"

Import and combine sample counts

all_sample_counts <- import_multiple_samples(folder_path = folder_path)

Define aggregation levels

taxonomic_level <- "domain" functional_level <- "main_module"

Aggregate counts

aggregated_counts <- aggregate_counts( all_sample_counts = all_sample_counts, ref_db = cereals_ref_db, taxonomic_level = taxonomic_level, functional_level = functional_level )