filter_taxa: Filter taxa based on across-sample OTU abundance criteria

In joey711/phyloseq: Handling and analysis of high-throughput microbiome census data

Filter taxa based on across-sample OTU abundance criteria

Description

This function is directly analogous to the genefilter function for microarray filtering, but is used for filtering OTUs from phyloseq objects. It applies an arbitrary set of functions — as a function list, for instance, created by filterfun — as across-sample criteria, one OTU at a time. It takes as input a phyloseq object, and returns a logical vector indicating whether or not each OTU passed the criteria. Alternatively, if the "prune" option is set to FALSE, it returns the already-trimmed version of the phyloseq object.

Usage

filter_taxa(physeq, flist, prune=FALSE)

Arguments

physeq	(Required). A phyloseq-class object that you want to trim/filter.
flist	(Required). A function or list of functions that take a vector of abundance values and return a logical. Some canned useful function types are included in the genefilter-package.
prune	(Optional). A logical. Default FALSE. If TRUE, then the function returns the pruned phyloseq-class object, rather than the logical vector of taxa that passed the filter.

Value

A logical vector equal to the number of taxa in physeq. This can be provided directly to prune_taxa as first argument. Alternatively, if prune==TRUE, the pruned phyloseq-class object is returned instead.

See Also

filterfun, genefilter_sample, filterfun_sample

Examples

 data("enterotype")
 require("genefilter")
 flist    <- filterfun(kOverA(5, 2e-05))
 ent.logi <- filter_taxa(enterotype, flist)
 ent.trim <- filter_taxa(enterotype, flist, TRUE)
 identical(ent.trim, prune_taxa(ent.logi, enterotype)) 
 identical(sum(ent.logi), ntaxa(ent.trim))
 filter_taxa(enterotype, flist, TRUE)

joey711/phyloseq documentation built on Nov. 4, 2022, 1:16 a.m.