Reads an OTU count table and a corresponding sintax taxonomy table from a USEARCH analysis pipeline, and then converts and combines them into an OTU table compatible with ampvis2.

amp_import_usearch(otutab, sintax)

Arguments

otutab

Path to the tabulated OTU count table as created by usearch10 -otutab ... -otutabout commands.

sintax

Path to the tabulated sintax taxonomy table as created by usearch10 -sintax ... -tabbedout commands.

Value

A data frame

Author

Kasper Skytte Andersen ksa@bio.aau.dk

Examples

if (FALSE) { # First import the usearch format OTU table: usearch_otutable <- amp_import_usearch( otutab = "/path/to/otutab.txt", sintax = "/path/to/sintax.txt" ) # Then use amp_load() with or without metadata as normal: d <- amp_load(usearch_otutable, metadata) }