[adegenet-forum] sPCA for environmental genomics

[Stéphane Dray]

Hi,

have a look to the adespatial package. It contains several tools (and 
references) for such type of analysis in the context of community ecology.

Cheers

Le 14/11/2018 à 19:59, Nicolas.Tsesmetzis at shell.com a écrit :
>
> Hello adegenet users,
>
> I am working in environmental genomics looking at microbial 
> communities in environmental samples (mostly soil). As each soil 
> sample can contain thousands of microorganisms (at different relative 
> abundances) we typically use Principal Coordinate Analysis (PCoA) to 
> identify samples that are similar to each other. What would be really 
> useful is if we could include geospatial information (Lat, Long) in 
> the analysis in order to determine whether the similarities in the 
> microbial profiles are due to their geospatial proximity (and the 
> underlying environmental parameters associated with that geographic 
> area).
>
> Searching for such type of analysis I came across the sPCA 
> functionality in the adegenet package. Is sPCA suitable for such 
> analysis? If so, would it be possible to retrofit the sPCA function in 
> adegenet to perform such analysis? If not, could anyone point me to a 
> tool (or a person) that could help me with this type of analysis?
>
> The input table is very simple:
>
> 	
>
> Organism 1
>
> 	
>
> Organism 2
>
> 	
>
> Organism 3
>
> 	
>
> ….
>
> 	
>
>  Organism m
>
> 	
>
> Lat
>
> 	
>
> Long
>
> Sample 1
>
> 	
>
> 0.5
>
> 	
>
> 0.1
>
> 	
>
> 0
>
> 	
>
> ….
>
> 	
>
> 0.2
>
> 	
>
> x1
>
> 	
>
> y1
>
> Sample 2
>
> 	
>
> 0.2
>
> 	
>
> 0
>
> 	
>
> 0
>
> 	
>
> ….
>
> 	
>
> 0.4
>
> 	
>
> x2
>
> 	
>
> y2
>
> Sample 3
>
> 	
>
> 0.1
>
> 	
>
> 0.8
>
> 	
>
> 0.6
>
> 	
>
> ….
>
> 	
>
> 0
>
> 	
>
> x3
>
> 	
>
> y3
>
> .
>
> 	
>
> .
>
> 	
>
> .
>
> 	
>
> .
>
> 	
>
> .
>
> 	
>
> .
>
> 	
>
> .
>
> 	
>
> .
>
> .
>
> 	
>
> .
>
> 	
>
> .
>
> 	
>
> .
>
> 	
>
> .
>
> 	
>
> .
>
> 	
>
> .
>
> 	
>
> .
>
> .
>
> 	
>
> .
>
> 	
>
> .
>
> 	
>
> .
>
> 	
>
> .
>
> 	
>
> .
>
> 	
>
> .
>
> 	
>
> .
>
> Sample n
>
> 	
>
> 0.06
>
> 	
>
> 0.1
>
> 	
>
> 0
>
> 	
>
> 	
>
> 0.2
>
> 	
>
> xn
>
> 	
>
> yn
>
> Total
>
> 	
>
> 1
>
> 	
>
> 1
>
> 	
>
> 1
>
> 	
>
> 	
>
> 1
>
> 	
>
> 	
>
>  Thank you all very much in advance for any pointers.
>
> Kind regards,
>
> *Nicolas Tsesmetzis, PhD*
> Shell International Exploration and Production Inc.
> 3333 Highway 6 South, P.O. Box 4685, Houston, Texas 77251-7171, USA
>
> *Tel:* +1 (281) 352-1475
> *Email:* nicolas.tsesmetzis at shell.com 
> <mailto:nicolas.tsesmetzis at shell.com>
>
> *Internet:* http://www.shell.com/eandp-en
>
>
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-- 
Stéphane DRAY (stephane.dray at univ-lyon1.fr)
Laboratoire BBE-CNRS-UMR-5558, Univ. C. Bernard - Lyon I
43, Bd du 11 Novembre 1918, 69622 Villeurbanne Cedex, France
http://pbil.univ-lyon1.fr/members/dray/
GdR EcoStat : https://sites.google.com/site/gdrecostat/


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