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agglomeration algorithm described in the manuscript: Mapping microbiota to clinical anxiety (Chin Fatt et al, unpublished).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.
devtools::install_github("SarahAsbury/retainresolve")
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
Higher quality PDF available also available for download in repository (retainresolve_algorithim.pdf).
mra = taxon mean relative abundance prev = taxon prevalence
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