pime.split.by.variable: Per variable slices

In microEcology/pime: Prevalence Interval for Microbiome Evaluation

Description

The used input file (in phyloseq object format) is sliced according to a metadata variable present in the metadata file. Code extracted from metagMisc: v.0.0.4 - DOI 10.5281/zenodo.172500

Usage

pime.split.by.variable(physeq, variable, drop_zeroes = T)

Arguments

physeq	The input file in phyloseq object format
variable	Any variable present in the metadata to be analyzed "variable to split"
drop_zeroes	Remove OTUs/ASVs with zeros, default is TRUE. If FALSE, OTUs with zero counts will be kept. Further analysis based on dissimilarity measurements (Bray-Curtis) might produce empty files.

Examples

phylist=pime.split.by.variable(restroom, "Environment")

microEcology/pime documentation built on Nov. 13, 2019, 11:16 p.m.