".xls") with both abundance and
taxonomy data. It also includes some confidence information related to the
taxonomic assignment.import_pyrotagger_tab(pyrotagger_tab_file,
strict_taxonomy=FALSE, keep_potential_chimeras=FALSE)FALSE. Should the taxonomyTable
component be limited to just taxonomic data? Default includes all fields from
the pyrotagger file.FALSE. The
pyrotagger output also includes OTUs that are tagged by pyrotagger as likely
chimeras. These putative chimeric OTUs can be retained if set to TRUE.
The putative chimeras are excluded by default.otuTax object containing both the otu_table and TaxonomyTable data
components, parsed from the pyrotagger output."http://pyrotagger.jgi-psf.org/"The typical output form PyroTagger is a spreadsheet format ".xls", which poses
additional import challenges. However, virtually all spreadsheet applications
support the ".xls" format, and can further export this file in a
tab-delimited format. It is recommended that you convert the xls-file without
any modification (as tempting as it might be once you have loaded it) into a
tab-delimited text file. Deselect any options to encapsulate fields in quotes,
as extra quotes around each cell's contents might cause problems during
file processing. These quotes will also inflate the file-size, so leave them out
as much as possible, while also resisting any temptation to modify the xls-file
``by hand''.
A highly-functional and free spreadsheet application can be obtained as part
of the cross-platform OpenOffice suite. It works for the above
required conversion. Go to "http://www.openoffice.org/".
It is regrettable that this importer does not take the xls-file directly
as input. However, because of the moving-target nature of spreadsheet
file formats, there is limited support for direct import of these formats into
R. Rather than add to the dependency requirements of emph{phyloseq}
and the relative support of these xls-support packages, it seems more efficient
to choose an arbitrary delimited text format, and focus on the data
structure in the PyroTagger output. This will be easier to support in the
long-run.
## New_otuTaxObject <- import_pyrotagger_tab(pyrotagger_tab_file)Run the code above in your browser using DataCamp Workspace