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@TuomasBorman @antagomir This is ready to merge |
TuomasBorman
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TuomasBorman
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Looks good! Couple points (see comments)
| Note that agglomeration by taxonomic rank might produce duplicate feature names, | ||
| such as "uncultured". If present, they can be made unique as follows: | ||
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Should this be handled by default, so that there should not be duplicated names?
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Do you mean model mofa should return an error/warning if names are duplicated? Or making them unique inside the mofa function?
I think users would better off make the names unique before running mofa, otherwise the link between original names and unique names is lost and users cannot trace the results back to their original set of features.
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Sorry, I checked this quickly.
I meant that
agglomerateByPrevalence() should output unique feature names by default
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Oh ok, so this chunk can be safely removed, correct?
Updated the grouping variable from 'Diet' to 'Fat' in the MOFA2 model.
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With this PR, the chapter on MOFA2 is updated to reflect the streamlined MOFA2 pipeline using the
mofa2wrapper that was recently implemented with this PR: bioFAM/MOFA2#144.