The strollur::write_phyloseq() function will take any strollur object and
return it as a phyloseq object.
References
McMurdie,P.J. and Holmes,S. (2013), phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data. PLoS ONE 8:e61217. doi:10.1371/journal.pone.0061217
Examples
miseq <- strollur::miseq_sop_example()
#> Added 2425 sequences.
#> Assigned 2425 sequence abundances.
#> Assigned 2425 sequence taxonomies.
#> Assigned 531 otu bins.
#> Assigned 2425 asv bins.
#> Assigned 63 phylotype bins.
#> Assigned 19 samples to treatments.
#> Assigned 171 samples distances.
#> Assigned 531 otu bin taxonomies.
#> Assigned 531 otu bin representative sequences.
#> Added a metadata report.
#> Added 2 resource references.
#> Added a contigs_report report.
if (requireNamespace("phyloseq", quietly = TRUE)) {
phylo_obj <- strollur::write_phyloseq(miseq)
} else {
message(paste(
"To use this functionality you have to install the",
"phyloseq package."
))
}