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
)

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

MiscMetabar documentation built on Oct. 8, 2024, 1:07 a.m.