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Verify the validity of a phyloseq object

Source: R/dada_phyloseq.R
verify_pq.Rd

lifecycle-maturing

Mostly for internal use in MiscMetabar functions.

Usage

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

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.

Value

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

Author

Adrien Taudière