View source: R/TaxonomicTable.R
TaxonomicTable | R Documentation |
The function assigns taxonomies (using USEARCH) for the reads, and creates taxonomic tables, as well as an annotated read table, in which all unique reads are assigned a taxonomy. Treating each unique read as a separate taxonomic unit offers the highest possible taxonomic resolution.
TaxonomicTable(usearch.path, refDB = system.file("extdata/silva_full.udb",package="mare"), folder.name = "", confidence.cutoff = 0.5)
usearch.path |
Directory of the USEARCH program. |
refDB |
Reference database. Defaults to the SILVA database that comes with mare. |
annotate.reads |
Should the reads be taxonomically annotated instead of the OTUs? TRUE is yes, FALSE if no. |
folder.name |
Name for the new folder where the taxonomic tables will be written. Should be the same as the folder.name given to function ProcessReads in order to analyse the correct reads. |
confidence.cutoff |
Lowest acceptable taxonomic confidence value. |
Katri Korpela
See http://drive5.com/usearch/manual/ for details on taxonomic annotation.
## Not run: #Taxonomically annotate the reads that are in folder ExampleProcessedReads, #using 0.6 confidence cut-off and a reference database created by FormatRefDB. #Then create taxonomic tables, which are written into a new folder called ExampleTaxonomicTables. TaxonomicTable(usearch.path = '/path/to/USEARCH8', reference.database = 'myrefDB.udb', folder.name = 'Example', confidence.cutoff = 0.6) ## End(Not run)
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