Phyloseq: How to add sample table to phyloseq object
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Brian Smith ▴ 120
@brian-smith-6197
Last seen 2.0 years ago
United States

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 ]

phyloseq sample_table phyloseq • 2.5k views
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Entering edit mode

Perhaps 4.7 years late but here is the answer to your question:

myobject@samdata <- sampledata(metadata)

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.

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