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

[Peter Solymos]

The tax_table accessor function will give you the taxonomic ranks in a
table according to this website:
https://web.stanford.edu/class/bios221/labs/phyloseq/lab_phyloseq.html
 otu_table will give you the data matrix with OTUs as *rows*. So you need
to transpose or adjust the code I suggested before.

Peter

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

> Hello,
> thank you for the replies. My dataset is something like this:
>
> > datafungi
>          BR1  BR2  BR3  BR4  BR5   F1   F2   F3   F4   F5   R1   R2   R3
> R4   R5   W1   W2   W3   W4   W5
> OTU_1   0.08 0.13 0.56 0.90 0.91 0.36 0.05 0.02 0.13 0.11 0.00 0.00 0.15
> 0.06 0.00 0.12 0.00 0.00 0.03 0.05
> OTU_35  0.01 0.01 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> 0.00 0.00 0.00 0.01 0.00 0.01 0.06
> OTU_4   0.01 0.00 0.00 0.00 0.00 0.00 0.01 0.31 0.08 0.00 0.07 0.05 0.00
> 0.00 0.00 0.00 0.00 0.07 0.41 0.00
> OTU_3   0.00 0.00 0.00 ...
>
> So I do not have the taxonomic hierarchy inside the normal dataset, but
> only the OTUs.
>
> Anyway, have taxonomic ranks embedded it in the phyloseq object:
>
> > fungi
> phyloseq-class experiment-level object
> otu_table()   OTU Table:         [ 150 taxa and 20 samples ]
> sample_data() Sample Data:       [ 20 samples by 5 sample variables ]
> tax_table()   Taxonomy Table:    [ 150 taxa by 7 taxonomic ranks ]
>
> That's I wondered why to do it using this kind of data. I think that many
> other researcher that work with huge species dataset (this one is not very
> big but I worked with thousands of OTUs) will have this problem.
> Do you have an idea how to deal with this kind of data object?
> Thank you,
> Gian
>
>
>
>
>
> On 25 June 2015 at 11:51, Peter Solymos <solymos at ualberta.ca
> <javascript:;>> wrote:
>
> > 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 <javascript:;>> 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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> >>
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> >
> >
> > --
> > --
> > Péter Sólymos
> > 780-492-8534 | solymos at ualberta.ca <javascript:;> | peter.solymos.org
> > Alberta Biodiversity Monitoring Institute http://www.abmi.ca
> > Boreal Avian Modelling Project http://www.borealbirds.ca
> >
> >
>
>
> --
>
>
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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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