The `read_phyloseq()` function reads phyloseq objects created from the phyloseq package (https://www.bioconductor.org/packages/release/bioc/html/phyloseq.html) and converts it into a strollur object.
Arguments
- phyloseq_object
the phyloseq object that is returned when using any read function in the phyloseq package. It has to be of type "phyloseq"
- treatment_column_name
the column name inside your phyloseq object within your sample data that is used to describe treatments. It must be a character. Defaults to NULL.
- dataset_name
A string containing a name for your dataset.
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 <- 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 531 otu bin taxonomies.
#> Assigned 531 otu bin representative sequences.
#> Added metadata.
#> Added 2 resource references.
#> Added a contigs_report.
if (requireNamespace("phyloseq", quietly = TRUE)) {
phylo_obj <- write_phyloseq(miseq)
miseq_re_read <- read_phyloseq(phylo_obj)
} else {
message(paste(
"To use this functionality you have to install the",
"phyloseq package."
))
}
#> Added 2425 sequences.
#> Assigned 2425 sequence abundances.
#> Assigned 2425 sequence taxonomies.
#> Added metadata.