search

nhanhocu / metamicrobiomeR

An R package for analysis of microbiome relative abundance data using zero inflated beta GAMLSS and meta-analysis across microbiome studies using random effects models
https://github.com/nhanhocu/metamicrobiomeR
33 stars 11 forks source link

Code seeking for taxa columns issue #14

Open raygozag opened 3 years ago

raygozag commented 3 years ago

The code expects k as part of the taxa column names, but qiime2 returns d as in "domain". This causes the code to fail without an obvious reason. maybe add a taxa column list as a parameter or throw an error no taxa were found or put this in the documentation. It may be better to specify the column list because other tools for fungi and so on don't use the same k__ taxonomy nomenclature.

nhanhocu commented 3 years ago

Hi, Thanks for trying the package and sorry for late response. A possible way for this situation is that you can specify/rename the taxanomy column names to be used with k_taxonomy.
In the long run, we will try to find time to revise the package to address this. Many thanks for your feedback.