This function removes ambiguous taxonomy names from specified ranks in a phyloseq object.
remove_ambiguous_taxa(phyloseq_obj, ranks, ambiguous_names)
| phyloseq_obj | A phyloseq object to filter. |
|---|---|
| ranks | A list of ranks to iterate over. |
| ambiguous_names | a list of ambiguous names to remove. |
Returns a phyloseq object without the ambiguous names in the specified ranks. MicrobiomeR was also written using the tidyverse in order to make the workflow reproducible.
This
tax_table, phy_tree, otu_table, sample_data, merge_phyloseq
filter, select, rownames, str_detect
Other Filters: preprocess_phyloseq
# NOT RUN {
> phy_obj <- get_phyloseq_object(...)
> phy_obj <- remove_ambiguous_taxa(phy_obj, list("Phylum", "Class", "Order"),
list("Unkown" , "Ambiguous", "uncultured"))
# }