filter_taxa

0th

Percentile

Filter taxa based on across-sample OTU abundance criteria

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

Aliases
  • filter_taxa
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)
Documentation reproduced from package phyloseq, version 1.16.2, License: AGPL-3

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