import_pyrotagger_tab: Imports a tab-delimited version of the pyrotagger output...

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

Imports a tab-delimited version of the pyrotagger output file.

Description

PyroTagger is a web-server that takes raw, barcoded 16S rRNA amplicon sequences and returns an excel spreadsheet (".xls") with both abundance and taxonomy data. It also includes some confidence information related to the taxonomic assignment.

Usage

import_pyrotagger_tab(pyrotagger_tab_file, 
strict_taxonomy=FALSE, keep_potential_chimeras=FALSE)

Arguments

pyrotagger_tab_file	(Required). A character string. The name of the tab-delimited pyrotagger output table.
strict_taxonomy	(Optional). Logical. Default FALSE. Should the taxonomyTable component be limited to just taxonomic data? Default includes all fields from the pyrotagger file.
keep_potential_chimeras	(Optional). Logical. Default 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.

Details

PyroTagger is created and maintained by the Joint Genome Institute at "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 emphphyloseq 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.

Value

An otuTax object containing both the otu_table and TaxonomyTable data components, parsed from the pyrotagger output.

References

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

Examples

## New_otuTaxObject <- import_pyrotagger_tab(pyrotagger_tab_file)

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