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

In joey711/phyloseq: Handling and analysis of high-throughput microbiome census data

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

joey711/phyloseq documentation built on Nov. 4, 2022, 1:16 a.m.