ANCOM-BC in QIIME2?

[tarandall (Tom Randall)]

Are there any plans to incorporate ANCOM-BC into future QIIME2 releases?

[Mehrbod_Estaki]

Hi @tarandall,

From the looks of it @mortonjt has already begin wrapping a q2-ancombc here, but I’m not sure if its currently complete, stable, or ongoing work. Keep an eye out on the forum, I’m sure when its ready to launch there will be a tutorial or post about it here.

[mortonjt (Jamie Morton)]

To answer @Mehrbod_Estaki’s comment, ANCOM-BC is still ongoing – we have a start, but now it mainly boils down to my unfamiliarity with R.

I recommend to take a look at the ANCOM-BC repo, particularly the unittests. If someone gets a script that can run ANCOM-BC directly from a biom table, then the plugin will more or less be ready.

[Lichen (Justin Shaffer)]

I've got this working, but the caveat is you have to start form a BIOM v.1 table.

[gibsramen (Gibraan Rahman)]

What's the limitation with other versions? I've run ANCOM-BC with a BIOM table (Gist) but I haven't generalized it. Also I don't recall the version of this BIOM table.

[Lichen (Justin Shaffer)]

I'm not exactly sure. When trying to import a contemporary BIOM table, I received the following error, which I believe derives from phyloseq. I think phyloseq is coded to handle BIOM v.1 tables, but not more recent versions.

Error in dimnames(x) <- dn :
length of 'dimnames' [2] not equal to array extent
In addition: There were 50 or more warnings (use warnings() to see the first 50)

[Mehrbod_Estaki]

Not ideal but phyloseq can accept any type of table, so converting any biom to a text file will get it in there too if needed.

[nathaniel_hubert]

Hello,

I just ran the commands below and got what looks to be good results (shows overlap with Spearman for the continuous variable).

The Github repository states these scripts draw heavily from the R documentation which I assume is well-tested. Is it premature to use the results in publication?

Thank you! ANCOM-BC seems an incredibly powerful tool, simultaneously offering multi-way differential abundance tests and allowing continuous independent variables.

qiime ancombc ancombc
--i-table table.qza
--m-metadata-file map.txt
--p-formula "category+continuous"
--o-differentials differentials.qza

qiime metadata tabulate
--m-input-file differentials.qza
--o-visualization differentials.qzv