phyloseq_filter_taxa_tot_fraction: Remove taxa with abundance less then a certain fraction of...

In vmikk/metagMisc: Miscellaneous functions for metagenomic analysis

Remove taxa with abundance less then a certain fraction of total abundance.

Description

Remove taxa with abundance less then a certain fraction of total abundance.

Usage

phyloseq_filter_taxa_tot_fraction(physeq, frac = 0.01)

Arguments

physeq	A phyloseq-class object
frac	The minimum cutoff for the OTU abundance in the table. This number is a fraction, not a percent.

Details

If frac = 0.0001, this will retain all OTU's that have at least a 0.01% total abundance in the OTU table. If you wanted to retain OTUs with at least 1% total abundance, you must specify, 0.01.

Value

Phyloseq object with a subset of taxa.

See Also

http://qiime.org/scripts/filter_otus_from_otu_table.html

Examples

data("esophagus")
phyloseq_filter_taxa_tot_fraction(esophagus, frac = 0.01)

vmikk/metagMisc documentation built on Feb. 14, 2024, 2:29 a.m.