[R-sig-eco] How to calculate relative abundance along taxonomical hierarchy

[Peter Solymos]

Gian,

Once you have your samples by OTU matrix row standardized, you can use a
level of your hierarchy (a vector matching the columns) and the
groupSums(your-matrix, 2, your-groups) function in the mefa4 package to get
your relative abundances.

Cheers,

Peter

Gian Maria Niccolò Benucci <gian.benucci at gmail.com> ezt írta (2015. június
25., csütörtök):

> Hello everyone,
> I am working on a fungal dataset with 151 OTUs distributed in 20 samples. I
> have imported it as phyloseq object and as normal species matrix as well to
> work with the vegan package.
> I am trying to find a way to get relative abundances at different
> hierarchical level goruping the abundances of the OTUs present in my
> dataset. For example, if I want to know what is the relative abundance of
> each Phylum (or of each Family, or each Genus) how can I do? There is a way
> to do that inside R?
> Thank you very much in advance,
>
>
> --
> ​Gian​
>
>
>
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-- 
--
Péter Sólymos
780-492-8534 | solymos at ualberta.ca | peter.solymos.org
Alberta Biodiversity Monitoring Institute http://www.abmi.ca
Boreal Avian Modelling Project http://www.borealbirds.ca

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