The bioBakery help forum

melonnPan questions

I recently read your paper “Predictive metabolomic profiling of microbial communities using amplicon or metagenomic sequences”, I was very impressed by the work done, and I am sure that melonnPan is a pivotal resource in the field of microbiome modeling. Being interested in it for my work, after reading the documentation and the tutorial, I decided to try obtaining some predictions with it. I was wondering if you could have time to help me with a couple of questions (or redirect me to whom to ask).

  1. In melonnpan.train what is exactly the train.metag input? I could not fully understand from the function description
  2. To obtain predictions with a previously trained model (different from the default one and obtained using melonnpan.train) is it enough to input a new weight matrix obtained using the melonnpan.train function?

Hi @sagunmaharjann - train.metag is the input metagenome file (e.g. gene families as profiled by HUMAnN2) which MelonnPan uses as predictors. To answer your second question, yes, it is sufficient to supply a new weight to get predictions from a newly trained model. Thanks!

Hi @himel.mallick and @sagunmaharjann, I asked a similiar question in another post MelonnPan training -- no common IDS
Could you please see? I am getting an error message if I input a new weight obtained from melonnpan.train()

@saif I just replied to the other thread. Let’s follow up either there or we can follow up here. Thanks!