% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/transform_filter-methods.R
\docType{methods}
\name{prune_taxa}
\alias{prune_taxa}
\alias{prune_taxa,NULL,ANY-method}
\alias{prune_taxa,logical,ANY-method}
\alias{prune_taxa,character,phylo-method}
\alias{prune_taxa,character,otu_table-method}
\alias{prune_taxa,character,sample_data-method}
\alias{prune_taxa,character,phyloseq-method}
\alias{prune_taxa,character,taxonomyTable-method}
\alias{prune_taxa,character,XStringSet-method}
\title{Prune unwanted OTUs / taxa from a phylogenetic object.}
\usage{
prune_taxa(taxa, x)

\S4method{prune_taxa}{`NULL`,ANY}(taxa, x)

\S4method{prune_taxa}{logical,ANY}(taxa, x)

\S4method{prune_taxa}{character,phylo}(taxa, x)

\S4method{prune_taxa}{character,otu_table}(taxa, x)

\S4method{prune_taxa}{character,sample_data}(taxa, x)

\S4method{prune_taxa}{character,phyloseq}(taxa, x)

\S4method{prune_taxa}{character,taxonomyTable}(taxa, x)

\S4method{prune_taxa}{character,XStringSet}(taxa, x)
}
\arguments{
\item{taxa}{(Required). A character vector of the taxa in object x that you want to
keep -- OR alternatively -- a logical vector where the kept taxa are TRUE, and length
is equal to the number of taxa in object x. If \code{taxa} is a named
logical, the taxa retained are based on those names. Make sure they are
compatible with the \code{taxa_names} of the object you are modifying (\code{x}).}

\item{x}{(Required). A phylogenetic object, including \code{phylo} trees,
as well as all phyloseq classes that represent taxa. If the function
\code{\link{taxa_names}} returns a non-\code{NULL} value, then your object
can be pruned by this function.}
}
\value{
The class of the object returned by \code{prune_taxa} matches
the class of the argument, \code{x}.
}
\description{
An S4 Generic method for removing (pruning) unwanted OTUs/taxa from phylogenetic
objects, including phylo-class trees, as well as native phyloseq package
objects. This is particularly useful for pruning a phyloseq object that has
more than one component that describes OTUs.
Credit: the \code{phylo}-class version is adapted from
\href{http://cran.at.r-project.org/web/packages/picante/index.html}{prune.sample}.
}
\examples{
data("esophagus")
esophagus
plot(sort(taxa_sums(esophagus), TRUE), type="h", ylim=c(0, 50))
x1 = prune_taxa(taxa_sums(esophagus) > 10, esophagus) 
x2 = prune_taxa(names(sort(taxa_sums(esophagus), TRUE))[1:9], esophagus) 
identical(x1, x2)
}
\seealso{
\code{\link{prune_samples}}

 \href{http://cran.at.r-project.org/web/packages/picante/index.html}{prune.sample}
}
