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How to generate D from phylogeneteic tree or data from qiime2? #14

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FSalOrt opened this issue Nov 16, 2024 · 0 comments
Open

How to generate D from phylogeneteic tree or data from qiime2? #14

FSalOrt opened this issue Nov 16, 2024 · 0 comments

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@FSalOrt
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FSalOrt commented Nov 16, 2024

Hi evryone!
I followed the instructions as the example and everything is ik, but i´m trying to do the same with my data (I have 16s sequencing data processed with qiime2 from different locations). But i don´t know how to generate D

mbImpute(condition = location, otu_tab = otu_table, metadata = manifest, D = ?)

as i read, D might be done with distance_mat function, but that function asks me for 3 inputs:
edges <- a matrix of dimension N*2 corresponding to the edge set of phylogenetic tree
n_taxa <- A scalar corresponding to number of taxa in the dataset
tree_height <- A scalar corresponding to the height of the phylogenetic tree.

And i dont know how to get those inputs.
I only have:
Representative sequences
otu table
metadata file
phylogenetic tree (made with iqtree within qiime2)

Does anyone if i might do the same as the example with my data?
thanks

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