TaxonomicTable: Create taxonomic tables

In katrikorpela/mare: Microbiota Analysis in R Easily

Create taxonomic tables

Description

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.

Usage

TaxonomicTable(usearch.path, 
              refDB = system.file("extdata/silva_full.udb",package="mare"), 
              folder.name = "", 
              confidence.cutoff = 0.5)

Arguments

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.

Author(s)

Katri Korpela

References

See http://drive5.com/usearch/manual/ for details on taxonomic annotation.

Examples

	## 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)

katrikorpela/mare documentation built on July 17, 2022, 2:49 a.m.