clst (version 1.20.0)

classifyPlacements: Taxonomic classification by phylogenetic placement.

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.

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