Calculate the relative abundance

[iordanis (H20)]

Hello, everyone.

There is any way that can i retained taxa that exceeded 5e−5 relative abundance with at least 10% prevalent in at least one study?

i found in qiime commands

qiime feature-table filter-features-conditionally \

--i-table relative-genus-feature-table.qza
--p-abundance 0.05
--p-prevalence 0.1
--o-filtered-table last-table.qza

but i understood that can calculate the prevalence for its sample!!

Can anyone knows?

or somehow that i can do it whit R?

thank for support!!!!

[colinvwood (Colin Wood)]

Hello @iordanis,

If you have samples from different studies in the same feature table and want to retain features according to prevalence within a single study not within the entire feature table, you can use feature-table split and then feature-table filter-features-conditionally on each table.

If I misunderstood what you're after let me know!

[iordanis (H20)]

Hello @colinvwood,

Thank for yours response.

You understood right!

One more question, i have ASV outputs. In command feature-table filter-features-conditionally, what data i must use?
I mean counts(absolute abundance) or (relative abundance). And after the processes, can i merged the table again? It is important for me to have one merged table for downstream analysis!

Jordan

[colinvwood (Colin Wood)]

Hello @iordanis,

You can use either absolute abundance (FeatureTable[Frequency]) or relative abundance (FeatureTable[RelativeFrequency]). Yes, you can merge the feature tables afterwards.

[iordanis (H20)]

@colinvwood

Thank you very much for the help!