import_uparse {phyloseq} | R Documentation

## 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.

### See Also

`import_usearch_uc`

### Examples

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[Package phyloseq version 1.28.0 Index]