Message-ID: <CAPxEaETTLns0TS4AW6My4eyyjfWias57sP-hZJecAt5NP-H3qA@mail.gmail.com>
Date: 2015-06-25T16:11:27Z
From: Gian Maria Niccolò Benucci
Subject: How to calculate relative abundance along taxonomical hierarchy
In-Reply-To: <CAH9coKYDMhDm0R=pGbLQhmMb--YshoP-aR_sQVz_J6HrpH-ctQ@mail.gmail.com>
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> 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 Niccol? Benucci <gian.benucci at gmail.com> ezt ?rta (2015.
> j?nius 25., cs?t?rt?k):
>
>> 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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>
>
> --
> --
> P?ter S?lymos
> 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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