subset_taxa-methods.Rd 1.65 KB
 Andreas Tille committed Sep 22, 2017 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 % Generated by roxygen2: do not edit by hand % Please edit documentation in R/taxonomyTable-class.R \docType{methods} \name{subset_taxa} \alias{subset_taxa} \title{Subset species by taxonomic expression} \usage{ subset_taxa(physeq, ...) } \arguments{ \item{physeq}{A \code{\link{taxonomyTable-class}}, or \code{\link{phyloseq-class}} that contains a taxonomyTable. If the \code{tax_table} slot is missing in \code{physeq}, then \code{physeq} will be returned as-is and a warning will be printed to screen.} \item{...}{The subsetting expression that should be applied to the \code{taxonomyTable}. This is passed on to \code{\link{subset}}, and more details and examples about how it functions can be found in its documentation.} } \value{ A subsetted object with the same class as \code{physeq}. } \description{ This is a convenience wrapper around the \code{\link{subset}} function. It is intended to speed subsetting complex experimental objects with one function call. In the case of \code{subset_taxa}, the subsetting will be based on an expression related to the columns and values within the \code{tax_table} (\code{taxonomyTable} component) slot of \code{physeq}. The \code{OTUs} retained in the dataset is equivalent to \code{x[subset & !is.na(subset)]}, where \code{x} is the vector of OTU IDs and \code{subset} is the logical that results from your subsetting expression. This is important to keep in mind, as users are often unaware that this subsetting step also removes/omits OTUs that have a missing value result, \code{NA}, somewhere in the expression. } \examples{ ## ex3 <- subset_taxa(GlobalPatterns, Phylum=="Bacteroidetes") } \seealso{ \code{\link{subset_samples}} }