import_uparse: Import UPARSE file format
In phyloseq: Handling and analysis of high-throughput microbiome census data

Description Usage Arguments Details See Also Examples

UPARSE is an algorithm for OTU-clustering implemented within usearch. At last check, the UPARSE algortihm was accessed via the -cluster_otu option flag. For details about installing and running usearch, please refer to the usearch website. For details about the output format, please refer to the uparse format definition.

1 2	import_uparse(upFile, omitChimeras = TRUE, countTable = TRUE, OTUtable = TRUE, verbose = TRUE)

`upFile`	(Required). A file location character string or `connection` corresponding to the file that contains the UPARSE output table. This is passed directly to `fread`. Please see its `file` argument documentation for further links and details.
`omitChimeras`	(Optional). `logical(1)`. Default is `TRUE`. Whether to omit entries that correspond to sequences/OTUs that were identified as chimeras.
`countTable`	(Optional). `logical(1)`. Default is `TRUE`. Whether to return the result as a wide-format table with dimensions OTU-by-sample, or to leave the table in its original sparse long-format that might be more suitable for certain `data.table` operations. If `TRUE`, entries corresponding to the same sample and OTU have their counts summed.
`OTUtable`	(Optional). `logical(1)`. Default is `TRUE`. Whether to coerce the result to `otu_table` format, or leave it as a `data.table` format. The former is appropriate for most `phyloseq` operations, the latter is useful for a lot of custom operations and custom `ggplot2` graphics calls.
`verbose`	(Optional). A `logical`. Default is `TRUE`. Should progresss messages be `cat`ted to standard out?

Because UPARSE is an external (non-R) application, there is no direct way to continuously check that these suggested arguments and file formats will remain in their current state. If there is a problem, please verify your version of usearch, create a small reproducible example of the problem, and post it as an issue on the phyloseq issues tracker.

import_usearch_uc