prune_taxaSamples: Prune a phyloseq object to exclude empty taxa/samples, which...

In sma-hsph/smar: Siyuan Ma's R code base

Prune a phyloseq object to exclude empty taxa/samples, which are prone to happen when a phyloseq object is subsetted.

Description

Prune a phyloseq object to exclude empty taxa/samples, which are prone to happen when a phyloseq object is subsetted.

Usage

prune_taxaSamples(physeq, flist_taxa = kOverA2(k = 1, A = 0),
  flist_samples = function(x) sum(x > 0) > 0, max.iter = 3)

Arguments

flist_taxa	function for filtering taxa, default to non-empty pruning
flist_samples	function for filtering sample, default to non-empty pruning
max.iter	maximum number of iterations

Value

the pruned phyloseq object

sma-hsph/smar documentation built on July 30, 2022, 2:34 p.m.