phyloseq: import_uparse – R documentation

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import_uparse

Import UPARSE file format

Description

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.

Usage

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

Arguments

`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?

Details

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.

Examples

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phyloseq

Handling and analysis of high-throughput microbiome census data

v1.34.0

AGPL-3

Authors

Paul J. McMurdie <joey711@gmail.com>, Susan Holmes <susan@stat.stanford.edu>, with contributions from Gregory Jordan and Scott Chamberlain

Initial release

2019-04-23