clean_pq {MiscMetabar} | R Documentation |
Clean phyloseq object by removing empty samples and taxa
Description
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_asv = FALSE,
rename_asv = FALSE,
simplify_taxo = FALSE
)
Arguments
physeq |
(required): a |
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_asv |
(logical) if TRUE the otu_table is ordered by the number of sequences of ASV (descending order). Default to FALSE. |
rename_asv |
(logical) if TRUE, ASV are renamed by their position in the OTU_table (asv_1, asv_2, ...). Default to FALSE. If rename ASV is true, the ASV names in verbose information can be misleading. |
simplify_taxo |
(logical) if TRUE, correct the taxonomy_table using the
|
Value
A new phyloseq-class
object