Assign Custom Mocks Taxonomy

assignTaxonomyCustomMock(
  x,
  mock_db = NULL,
  processors = NULL,
  threshold = 60,
  strand = "top",
  verbose = FALSE,
  ...
)

Arguments

x: Phyloseq objects where taxa_names are ASV sequences
mock_db: ZymoTrainingSet
processors: Passed on to DECIPHER::IdTaxa Default is NULL
threshold: Passed on to DECIPHER::IdTaxa. Default is 60
strand: DECIPHER::IdTaxa Default is top
verbose: Default is FALSE
...: Arguments to pass on to DECIPHER::IdTaxa

Value

Phyloseq with new taxonomy

Details

For consistency in taxonomic assignments, use only a small database that has 16S rRNA gene sequences from mock community genomes. This is done to avoid any clashes/changes that happen with public databases and to get a direct comparison.

Author

Sudarshan Shetty sudarshanshetty9@gmail.com

Examples

#output.dat <- assignTaxonomyCustomMock(ps.zym,
 #                                      mock_db = NULL,
  #                                     processors = 2,
   #                                    threshold = 80)