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biocore / songbird

Vanilla regression methods for microbiome differential abundance analysis
BSD 3-Clause "New" or "Revised" License
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using a subset of samples #142

Closed coralzhang closed 3 years ago

coralzhang commented 3 years ago

Hi I wonder if there is a way to run the songbird only on a subset of the biom file- say if, in the metadata file, I have a variable, and I only want to run the model on the samples with this variable equals to 1. Thanks for your time!

mortonjt commented 3 years ago

Definitely. You can either subset your metadata table, or filter your biom table. See the qiime2 filtering data tutorials for examples : https://docs.qiime2.org/2020.8/tutorials/filtering/

On Fri, Oct 23, 2020 at 1:18 PM coralzhang notifications@github.com wrote:

Hi I wonder if there is a way to run the songbird only on a subset of the biom file- say if, in the metadata file, I have a variable, and I only want to run the model on the samples with this variable equals to 1. Thanks for your time!

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coralzhang commented 3 years ago

So, songbird itself does not do that, and it has to be through qiime2?

mortonjt commented 3 years ago

Right

On Fri, Oct 23, 2020 at 1:42 PM coralzhang notifications@github.com wrote:

So, songbird itself does not do that, and it has to be through qiime2?

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