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biocore / songbird

Vanilla regression methods for microbiome differential abundance analysis
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Accounting for phylogenetic relation between samples in the formula? #97

Open Jigyasa3 opened 4 years ago

Jigyasa3 commented 4 years ago

Hey!

I have two questions-

  1. I have a biom file of microbial KEGG pathways for 100 host samples which are phylogenetically related. I was wondering if I can account for phylogenetic relation between host samples in the co-variates via patristic distance?

For example, --formula "Depth+Temperature+patristic(phy)"

  1. Are the other flags (as given below) default in songbird command? --epochs 10000 \ --differential-prior 0.5 \ --summary-interval 1 \
mortonjt commented 4 years ago

Question 1 : See our paper on phylogenetic methods. It sounds like you want something like phylogenetic GLS - but it's not clear to me.

I suggest looking at phylofactor : https://github.com/reptalex/phylofactor

Songbird does not support phylogenetic methods, and won't for the foreseeable future.

Question 2 : the defaults should be in the command. Does it show when you run it on the command line?

On Tue, Nov 12, 2019, 1:31 AM Jigyasa3 notifications@github.com wrote:

Hey!

I have two questions-

  1. I have a biom file of microbial KEGG pathways for 100 host samples which are phylogenetically related. I was wondering if I can account for phylogenetic relation between host samples in the co-variates via patristic distance?

For example, --formula "Depth+Temperature+patristic(phy)"

  1. Are the other flags (as given below) default in songbird command? --epochs 10000 --differential-prior 0.5 --summary-interval 1 \

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