README.md

In SarahAsbury/retainresolve: Retain Resolve Microbiome Agglomeration

retainresolve

Retain-resolve agglomeration algorithim for 16S sequencing data.

## About

This R package has been developed to conveniently execute the retain-resolve agglomeration algorithm described in the manuscript: Mapping microbiota to clinical anxiety (Chin Fatt et al, unpublished). The retain resolve algorithm requires ASV-level 16S count data stored as a phyloseq object. Users input parameters for ASV-level and genus-level filtering thresholds. The main output is a phyloseq object containing a mix of retained ASV-level and resolved genus-level taxa and their counts.

Install

devtools::install_github("SarahAsbury/retainresolve")

Use

Once package is installed, use following command in R for retain-resolve function documenation and examples:

?retain.resolve_genus

Documentation and examples are also available at: https://rdrr.io/github/SarahAsbury/retainresolve/man/retain.resolve_genus.html

Summary

Higher quality PDF available also available for download in repository (retainresolve_algorithim.pdf).

Example of mean relative abundance and prevalence distributions after retain-resolve

mra = taxon mean relative abundance prev = taxon prevalence

SarahAsbury/retainresolve documentation built on Feb. 20, 2023, 7:48 a.m.