I am trying to create an ASV table where the abundances of my replicates are averaged. However, I haven't figured out how to do this. This was possible in phyloseq with merge_samples(phyloseq_object,"variable", fun = mean ) but now fun=mean doesn't work. You can only get the sum of the abundances.
Any idea how I can do this in R?
Also, how do we get an averaged ASV table if we want to perform any transformations like log transformation prior to averaging?
Hi @uth ,
I can tell you how to do this in QIIME 2. If you have your replicates in a single table, you can use qiime feature-table group to group these samples together (based on a sample metadata column that specifies the samples that each replicate belongs to). You can take the mean, median, or sum of the grouped samples.
This action only works on FeatureTable[Frequency] type tables, so cannot be used with log-transformed tables.
Thank you so much @Nicholas_Bokulich for you reply. Reason why I was looking to do this in R instead of Qiime2 is that I run "decontam" on my samples in R. I prefer to get rid of the contaminants and then average the ASVs.