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zdk123 / SpiecEasi

Sparse InversE Covariance estimation for Ecological Association and Statistical Inference
GNU General Public License v3.0
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Better feature labelling for output networks #137

Open ntromas opened 3 years ago

ntromas commented 3 years ago

Hi,

Thanks for the tutorial! I would like to determine the co-occurrence between two different composition from the same samples (I used two different amplicon sequencing approach from the same samples). I wonder if, in that case, it is possible to extract the correlation or covariance matrix with ASV names. I am not sure about to what correspond the order as I have two phyloseq element and I am not sure how to extract properly this matrix. I tried as.matrix(symBeta(getOptBeta(result_spieceasi).

Thanks for your help!

Cheers,

Nico

zdk123 commented 3 years ago

Yes, a labelled output network is requested a lot so I'll add it in the next release. However the output OTU order is the same as the input order. For multi-"domain" it should just be the first dataset concatenated with the second dataset.

ntromas commented 3 years ago

Ok thanks!