I got a biom table resulted after running Dada2 in Qiime2. Now I want to analyse the microbiome using the Vegan package for R. In addition I would like to use the MicrobiomeAnalyst web server (https://www.microbiomeanalyst.ca/) which includes pipelines to obtain a metabolic profile of each sample.
Could someone tell me how I have to treat those data to apply the functions in R. The biom table has to be transformed into another table?
Did anyone use the MicrobiomeAnalyst web server?
thank you in advance
Dear Jose,
Functions in package 'vegan' need input data.frame (or a dissimilarity matrix based on such data.frame) with the following structure:
- entities to be compared (called 'sites' by vegan) in the rows, and
- characteristics (called 'species') in the columns.
Vegan was written for vegetation analysis (this is why it uses misleading names for the entities and characteristics), but can be used for any dataset that is provided in the appropriate structure.
I'm not familiar with MicrobiomeAnalyst, but am sure that its result can be transformed somehow to the desired structure.
HTH,
Ákos
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