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.
filter_taxa(physeq, flist, prune=FALSE)
physeq |
(Required). A |
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 |
prune |
(Optional). A logical. Default |
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.
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)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.