taxonomyFromRefpkg: Extract taxonomic information from a refpkg.
In clstutils: Tools for performing taxonomic assignment.

Description Usage Arguments Value Author(s) References See Also Examples

Construct a data.frame providing the lineage of each sequence represented in the reference package.

1	taxonomyFromRefpkg(path, seqnames, lowest_rank = NA)

`path`	path to a refpkg directory
`seqnames`	optional character vector of sequence names. If provided, determines the order of rows in `$taxTab`
`lowest_rank`	name of the most specific (ie, rightmost) rank to include. Default is the name of the rightmost column in `refpkg_contents$taxonomy`

A list with the following elements:

`taxNames`	a named character vector of taxonomic names (names are tax_ids)
`taxTab`	a `data.frame` in which each row corresponds to a reference sequence and contains a tax_id followed by the corresponding lineage (columns are "root"...lowest_rank)

Noah Hoffman

The decsription and specification for a reference package can be found in the project repository in github: https://github.com/fhcrc/taxtastic

Scripts and tools for creating reference packages are provided in the python package taxonomy, also available from the taxtastic project site.

refpkgContents

archive <- 'vaginal_16s.refpkg.tar.gz'
destdir <- tempdir()
system(gettextf('tar -xzf %s --directory="%s"',
                system.file('extdata',archive,package='clstutils'),
                destdir))
refpkg <- file.path(destdir, sub('.tar.gz','',archive))
reftax <- taxonomyFromRefpkg(refpkg)
str(reftax)

Loading required package: clst
Loading required package: rjson
Loading required package: ape
List of 2
 $ taxNames: Named chr [1:281] "root" "cellular organisms" "Bacteria" "unclassified Bacteria" ...
  ..- attr(*, "names")= chr [1:281] "1" "131567" "2" "2323" ...
 $ taxTab  :'data.frame':	652 obs. of  22 variables:
  ..$ tax_id                  : chr [1:652] "103621" "103621" "103621" "109790" ...
  ..$ root                    : chr [1:652] "1" "1" "1" "1" ...
  ..$ below_root              : chr [1:652] "131567" "131567" "131567" "131567" ...
  ..$ superkingdom            : chr [1:652] "2" "2" "2" "2" ...
  ..$ below_superkingdom      : chr [1:652] NA NA NA NA ...
  ..$ below_below_superkingdom: chr [1:652] NA NA NA NA ...
  ..$ superphylum             : chr [1:652] NA NA NA NA ...
  ..$ phylum                  : chr [1:652] "201174" "201174" "201174" "1239" ...
  ..$ subphylum               : chr [1:652] NA NA NA NA ...
  ..$ class                   : chr [1:652] "1760" "1760" "1760" "91061" ...
  ..$ subclass                : chr [1:652] "85003" "85003" "85003" NA ...
  ..$ order                   : chr [1:652] "2037" "2037" "2037" "186826" ...
  ..$ below_order             : chr [1:652] NA NA NA NA ...
  ..$ below_below_order       : chr [1:652] NA NA NA NA ...
  ..$ suborder                : chr [1:652] "85005" "85005" "85005" NA ...
  ..$ family                  : chr [1:652] "2049" "2049" "2049" "33958" ...
  ..$ below_family            : chr [1:652] NA NA NA NA ...
  ..$ genus                   : chr [1:652] "1654" "1654" "1654" "1578" ...
  ..$ species_group           : chr [1:652] NA NA NA NA ...
  ..$ species_subgroup        : chr [1:652] NA NA NA NA ...
  ..$ species                 : chr [1:652] "103621" "103621" "103621" "109790" ...
  ..$ below_species           : chr [1:652] NA NA NA NA ...