subset_samples_no_zero: Subset samples and prune taxa/OTU with zero abundance

In cpauvert/psadd: Additions to phyloseq package for microbiome analysis

Description

Subset samples and prune taxa/OTU with zero abundance

Usage

subset_samples_no_zero(physeq, ...)

Arguments

physeq	otu_table-class, or phyloseq-class
...	The subsetting expression that should be applied to the sampleTable. This is passed on to subset_samples. Note that taxa/OTU with zero abundance are pruned from the phyloseq-class object.

Value

A subsetted object with the same class as physeq

See Also

subset_samples on which it rely.

Examples

require(phyloseq)
data(GlobalPatterns)
gp<-subset_samples(GlobalPatterns, SampleType=="Ocean")
gp.nz<-subset_samples_no_zero(GlobalPatterns, SampleType=="Ocean")
ntaxa(gp) # 19216 OTU
ntaxa(gp.nz) # 5669 OTU

cpauvert/psadd documentation built on Nov. 22, 2020, 9:19 a.m.