classifyPlacements {clstutils} | R Documentation |
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
.
classifyPlacements(taxdata, treedists, placetab, ..., verbose = FALSE, debug = FALSE)
taxdata |
|
treedists |
output of |
placetab |
a data.frame with columns |
... |
extra arguments passed to |
verbose |
writes progress messages to terminal if TRUE |
debug |
be very verbose if TRUE |
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.
Noah Hoffman
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