Verify the validity of a phyloseq object — verify

Mostly for internal use in MiscMetabar functions.

Usage

verify_pq(
  physeq,
  verbose = FALSE,
  min_nb_seq_sample = 500,
  min_nb_seq_taxa = 1,
  check_taxonomy = FALSE,
  ...
)

Arguments

physeq: (required) a phyloseq-class object obtained using the phyloseq package.
verbose: (logical, default FALSE) If TRUE, prompt some warnings.
min_nb_seq_sample: (numeric) Only used if verbose = TRUE. Minimum number of sequences per samples to not show warning.
min_nb_seq_taxa: (numeric) Only used if verbose = TRUE. Minimum number of sequences per taxa to not show warning.
check_taxonomy: (logical, default FALSE) If TRUE, call verify_tax_table() to check for common taxonomy table issues.
...: Additional arguments passed to verify_tax_table() when check_taxonomy = TRUE.

Value

Nothing if the phyloseq object is valid. An error in the other case. Warnings if verbose = TRUE or check_taxonomy = TRUE

Author

Adrien Taudière

Examples


verify_pq(data_fungi)
# \donttest{
verify_pq(data_fungi, check_taxonomy = TRUE)
#> Warning: Found 145 taxonomic value(s) matching NA-like patterns. Unique values: Pezizomycotina_cls_Incertae_sedis, Rozellomycotina_cls_Incertae_sedis, Sordariomycetes_ord_Incertae_sedis, Microbotryomycetes_ord_Incertae_sedis, Lecanoromycetes_ord_Incertae_sedis, Dothideomycetes_ord_Incertae_sedis, Cystobasidiomycetes_ord_Incertae_sedis, Pezizomycotina_ord_Incertae_sedis, Cantharellales_fam_Incertae_sedis, Atractiellales_fam_Incertae_sedis, .... Use modify_phyloseq = TRUE to replace these with NA.
#> Warning: Found 1432 taxonomic value(s) with less than 4 characters: - (Trophic.Mode, 1 chars), - (Guild, 1 chars), - (Trait, 1 chars), - (Confidence.Ranking, 1 chars). Use modify_phyloseq = TRUE to replace these with NA.
#> Found 976 taxa with duplicate taxonomic paths. This may indicate redundant taxa or issues with taxonomic assignment.
#> Warning: Found 1319 taxonomic value(s) with internal spaces: 'Plant Pathogen' (Guild), 'Endophyte-Undefined Saprotroph-Wood Saprotroph' (Guild), 'Wood Saprotroph-Undefined Saprotroph' (Guild), 'Undefined Saprotroph' (Guild), 'Wood Saprotroph' (Guild), .... Use modify_phyloseq = TRUE and remove_all_space = TRUE to replace these spaces with '_'.
# }