phyloseq_filter_abundant_taxa: Filter a phyloseq table keeping only abundant taxa

In vaulot/dvutils: A set of utilities

Description

Filter a phyloseq table keeping only abundant taxa

Usage

phyloseq_filter_abundant_taxa(ps, fraction_min = 0.1)

Arguments

ps	phyloseq object
fraction_min	minimum fraction that an OTU must represent in any given samples (not overall!) - 0.10 corresponds to 10%

Value

ps object with only abundant taxa

Examples

# Will return the otus that more that represent more than 10% of total in any given sample. It also normalize the phyloseq to the median of the remaining OTUs
ps_abundant <- phyloseq_filter_abundant_taxa(ps)
# Idem but with lower threshold (5%)
ps_abundant <- phyloseq_filter_abundant_taxa(ps, 0.05)

vaulot/dvutils documentation built on Nov. 20, 2021, 11:01 a.m.