rm_nonbac: Removal of non-bacterial sequences from a phyloseq object

In peterolah001/BiMiCo: Biomap Microbiome Core methods

Removal of non-bacterial sequences from a phyloseq object

Description

Given an input phyloseq object with valid tax_table, returns taxonomy-filtered phyloseq object with mitochondrial, chloroplast and non-bacterial taxa removed. Non-bacterial sequences (e.g. mitochondria, chloroplast) need to be removed from OTU/ASV tables prior to statistical analyses. rm_nonbac removes all rows of otu_table and tax_table in a phyloseq object based on taxonomic labelling 'Mitochondria', 'Chloroplast' or where Kingdom is other than 'Bacteria'. NAs in taxonomy table are converted to 'unidentified'.

Usage

rm_nonbac(x)

Arguments

x	Phyloseq object with non-empty otu_table and tax_table slots; otu_table may contain either OTUs or ASVs.

Examples

rm_nonbac()

peterolah001/BiMiCo documentation built on April 24, 2023, 3:35 a.m.