import {phyloseq} | R Documentation

## Universal import method (wrapper) for phyloseq-package

### Description

A user must still understand the additional arguments required for each type of import data. Those arguments are described in detail at the tool-specific `import_*` links below. Each clustering tool / package / pipeline has its own idiosyncratic set of file names / types, and it remains the responsibility of the user to understand which file-path should be provided to each argument for the particular importing submethod. This method merely provides a central documentation and method-name, and the arguments are passed along as-is.

### Usage

    import(pipelineName, ...)

### Arguments

`pipelineName` | (Required). Character string. The name of the analysis tool / pipeline / package that created the OTU-cluster data or other data that you now want to import. Current options are `c("mothur", "pyrotagger", "QIIME", "RDP")`, and only the first letter is necessary.
`...` | (Required). Additional named arguments providing file paths, and possible other paramaters to the desired tool-specific import function.

### Value

In most cases a `phyloseq-class` will be returned, though the included component data will vary by pipeline/tool, and also by the types of data files provided. The expected behavior is to return the most-comprehensive object possible, given the provided arguments and pipeline/tool.

### References

BIOM: http://www.biom-format.org/

mothur: http://www.mothur.org/wiki/Main_Page

PyroTagger: http://pyrotagger.jgi-psf.org/

QIIME: http://qiime.org/

RDP pipeline: http://pyro.cme.msu.edu/index.jsp

### See Also

For BIOM format, see: `import_biom`

For mothur, see: `import_mothur`

Separate tools for mothur are also: `show_mothur_cutoffs` `import_mothur_dist` `export_mothur_dist`

For PyroTagger, see: `import_pyrotagger_tab`

For QIIME legacy format, see: `import_qiime`

For RDP pipeline, see: `import_RDP_cluster`

`import_RDP_otu`

### Examples

     ## See documentation of a specific import function

[Package phyloseq version 1.26.1 Index]