Entering edit mode
Hi,
My QIIME biom output only has OTU and taxa tables (see below). How can I add a sample_table to my phyloseq object?
thanks!
> myboject = import_biom(biomfile, parseFunction = parse_taxonomy_greengenes)
> myobject
phyloseq-class experiment-level object
otu_table() OTU Table: [ 3576 taxa and 132 samples ]
tax_table() Taxonomy Table: [ 3576 taxa by 7 taxonomic ranks ]
Perhaps 4.7 years late but here is the answer to your question:
where metadata is, of course, your metadata (sample data) previously imported into your R session and properly formated. This metadata file must have the names of the samples as row names, and the samples order must match the exact same order from your OTU/taxa table.
Oscar.