Data quality control - filter by otu_props

[filipam...@gmail.com]

Hello, 

is there a way of filtering low-abundance OTUs by otu_props instead of counts?

congratulations for the package and thanks for the thoughtful manuals.

thanks. kindest regards,

Filipa

[Zachary Foster]

Hello Filipa,

Thanks!

Yes, OTU data is usually a table and you can filter a table on any per-row information, such as counts or proportions, assuming you have that information. Similarity, you can filter taxa by per-taxon information. How you would do that exactly depends on how you data is formatted, but in general, for OTU data, you would filter rows in the table using standard R subsetting ( my_taxmap$data$my_table[my_taxmap$data$my_table$prop > 0.01, ]) or dplyr filter methods ( filter(my_taxmap$data$my_table, prop > 0.01) ) and taxa are filtered using "filter_taxa" ( filter_taxa(my_taxmap, tax_prop > 0.001) ).

If you send me an example of your data/code, I can give you more specific advice.

Best,

Zach