Cluster ASVs into Clusters

Arguments

x: A phyloseq object
cluster_method: See methods in IdClusters in DECIPHER Default is "inexact"
cluster_cutoff: Cut-off for clustering ASVs. Default= 0.01 i.e. 99 percent identity
threads: No. of processors to use

Value

A new phyloseq object with cluster ASVs

Details

clusterASVs clusters ASV sequences obtained after dada2 in phyloseq object into clusters based on user provided sequence identity. If using method="inexact" this is similar to OTU approach for example clustering of ASVs that are 97 for ASVs or OTUs is highly debated (see reference section), both have their pros and cons.The user is advised to make appropriate choice based on their research questions and properties of data.

References

Clustering ASVs after DADA2? generating new OTU table. GitHub issue #947: https://github.com/benjjneb/dada2/issues/947
Michael McLaren. mikemc/speedyseq: speedyseq v0.2.0. Zenodo, 2020, June 30, (Version v0.2.0). http://doi.org/10.5281/zenodo.3923184
PD Schloss. Pre-print Review of 97 Blogpost: The Academic Hermit, 2017, Oct 11. http://www.academichermit.com/2017/10/11/Review-of-Updating-the-97-identity-threshold.html
Angela Oliverio and Noah Fierer. Intragenomic heterogeneity and its implications for ESVs. Blogpost: Fierer Lab, 2017, Oct 9. http://fiererlab.org/2017/10/09/intragenomic-heterogeneity-and-its-implications-for-esvs/
Noah Fierer, Tess Brewer, and Mallory Choudoir. Lumping versus splitting – is it time for microbial ecologists to abandon OTUs?. Blogpost: Fierer Lab, 2017, May 2. http://fiererlab.org/2017/05/02/lumping-versus-splitting-is-it-time-for-microbial-ecologists-to-abandon-otus/

Author

Sudarshan A. Shetty

Examples

if (FALSE) {
library(biomeUtils)
library(dplyr)
library(data.table)
library(tibble)

testSprockett <- core(subset_samples(SprockettTHData, Community == "River_4"), 5, 20 / 100)
testSprockett <- clusterASVs(testSprockett,
                             cluster_cutoff = 0.01,
                             threads = 2)
}