phyloseq_sep_variable: Split phyloseq-class object by sample-level variable.

In vmikk/metagMisc: Miscellaneous functions for metagenomic analysis

Split phyloseq-class object by sample-level variable.

Description

This function splits a phyloseq object by sample meta-data, returning a list of objects whose components each correspond to a group of samples.

Usage

phyloseq_sep_variable(physeq, variable, drop_zeroes = T)

Arguments

physeq	A phyloseq-class object
variable	Variable name (contained in sample_data)
drop_zeroes	Logical, indicating weather OTUs with zero abundance withing a group of samples should be removed

Value

List with phyloseq objects.

Examples

data(GlobalPatterns)

# Split data by sample type (e.g., Soil, Ocean, etc.)
phyloseq_sep_variable(GlobalPatterns, variable = "SampleType")

# Do not remove OTUs with total zero abundance within each sample type
phyloseq_sep_variable(GlobalPatterns, variable = "SampleType", drop_zeroes = FALSE)

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