classifyPlacements: Taxonomic classification by phylogenetic placement.

In clstutils: Tools for performing taxonomic assignment.

Description

Given taxonomic information from a reference package and inter-node distances from a reference tree, perform classification of one or more placements provided by pplacer.

Usage

classifyPlacements(taxdata, treedists, placetab, ...,
    verbose = FALSE, debug = FALSE)

Arguments

taxdata	data.frame, output of taxonomyFromRefpkg
treedists	output of treeDists
placetab	a data.frame with columns at, edge, and branch
...	extra arguments passed to classifyIter
verbose	writes progress messages to terminal if TRUE
debug	be very verbose if TRUE

Value

The output is a data.frame describing the taxonomic assignment, along with a description of the confidence of the classification. See the man page for classify for details on the output.

Author(s)

Noah Hoffman

See Also

treeDists, taxonomyFromRefpkg

Examples

placefile <- system.file('extdata', 'merged.json', package='clstutils')
distfile <- system.file('extdata', 'merged.distmat.bz2', package='clstutils')
refpkgz <- system.file('extdata', 'vaginal_16s.refpkg.tar.gz', package='clstutils')

tmpdir <- tempdir()

orig.dir <- getwd()
setwd(tmpdir)
system(paste("tar --no-same-owner -xzf", refpkgz))
setwd(orig.dir)


refpkg <- file.path(tmpdir, "vaginal_16s.refpkg")

treedists <- treeDists(distfile=distfile, placefile=placefile)
taxdata <- taxonomyFromRefpkg(refpkg, seqnames=rownames(treedists$dmat), lowest_rank="species")
placetab <- data.frame(at=49, edge=5.14909e-07, branch=5.14909e-07)
result <- classifyPlacements(taxdata, treedists, placetab)
result

clstutils documentation built on Nov. 8, 2020, 5:23 p.m.