verify_pq: Verify the validity of a phyloseq object

In MiscMetabar: Miscellaneous Functions for Metabarcoding Analysis

Verify the validity of a phyloseq object

Description

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(s)

Adrien Taudière

Examples

verify_pq(data_fungi_mini)

verify_pq(data_fungi_mini, check_taxonomy = TRUE)

MiscMetabar documentation built on June 8, 2026, 5:07 p.m.