Skip to contents

Clean phyloseq object by removing empty samples and taxa

Source: R/dada_phyloseq.R
clean_pq.Rd

lifecycle-experimental

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",
  check_taxonomy = FALSE
)

Arguments

physeq

(required) a phyloseq-class object obtained using the phyloseq package.

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, default FALSE) if TRUE, taxa (ASV, OTU) are renamed by their position in the OTU_table and prefix_taxa_names param (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_")

check_taxonomy

(logical, default FALSE) If TRUE, call verify_tax_table() to check for common taxonomy table issues.

Value

A new phyloseq-class object

Author

Adrien Taudière

Examples

clean_pq(data_fungi_mini)
#> phyloseq-class experiment-level object
#> otu_table()   OTU Table:         [ 45 taxa and 137 samples ]
#> sample_data() Sample Data:       [ 137 samples by 7 sample variables ]
#> tax_table()   Taxonomy Table:    [ 45 taxa by 12 taxonomic ranks ]
#> refseq()      DNAStringSet:      [ 45 reference sequences ]