I have phyloseq object where sequence table were builded by using the function mergeSequenceTables from DADA2 package, to merge ten sequence tables from different runs.
The sample_data consist of two columns 1)containing sample names same as sequence table column names and 2)study name from which samples comes from.
Using this information I want to filter the genera from all phyloseq object to have at least 3 studies the average abundance > 10%.
It is important to mention that sequence table sequences can be assigned to same genus in tax_table.
Does anyone have any pointers?
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