classifyPlacements {clstutils} | R Documentation

## 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.

### 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

[Package clstutils version 1.42.0 Index]