In addition, this function check for discrepancy (and rename) between (i) taxa names in refseq, taxonomy table and otu_table and between (ii) sample names in sam_data and otu_table.
Usage
clean_pq(
physeq,
remove_empty_samples = TRUE,
remove_empty_taxa = TRUE,
clean_samples_names = TRUE,
silent = FALSE,
verbose = FALSE,
force_taxa_as_columns = FALSE,
force_taxa_as_rows = FALSE,
reorder_taxa = FALSE,
rename_taxa = FALSE,
simplify_taxo = FALSE,
prefix_taxa_names = "_Taxa"
)Arguments
- physeq
(required): a
phyloseq-classobject obtained using thephyloseqpackage.- remove_empty_samples
(logical) Do you want to remove samples without sequences (this is done after removing empty taxa)
- remove_empty_taxa
(logical) Do you want to remove taxa without sequences (this is done before removing empty samples)
- clean_samples_names
(logical) Do you want to clean samples names?
- silent
(logical) If true, no message are printing.
- verbose
(logical) Additional informations in the message the verbose parameter overwrite the silent parameter.
- force_taxa_as_columns
(logical) If true, if the taxa are rows transpose the otu_table and set taxa_are_rows to false
- force_taxa_as_rows
(logical) If true, if the taxa are columns transpose the otu_table and set taxa_are_rows to true
- reorder_taxa
(logical) if TRUE the otu_table is ordered by the number of sequences of taxa (ASV, OTU) in descending order. Default to FALSE.
- rename_taxa
(logical) if TRUE, taxa (ASV, OTU) are renamed by their position in the OTU_table and prefix_taxa_names param (by default: Taxa_1, Taxa_2, ...). Default to FALSE. If rename taxa (ASV, OTU) is true, the taxa (ASV, OTU) names in verbose information can be misleading.
- simplify_taxo
(logical) if TRUE, correct the taxonomy_table using the
MiscMetabar::simplify_taxo()function- prefix_taxa_names
(default "Taxa_"): the prefix of taxa names (eg. "ASV_" or "OTU_")
Value
A new phyloseq-class object