Universal import method (wrapper) for phyloseq-package
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.
import(pipelineName, ...)
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 |
... |
(Required). Additional named arguments providing file paths, and possible other paramaters to the desired tool-specific import function. |
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.
PyroTagger: http://pyrotagger.jgi-psf.org/
QIIME: http://qiime.org/
RDP pipeline: http://pyro.cme.msu.edu/index.jsp
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
## See documentation of a specific import function
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