A use case I sometimes find myself in when analyzing taxonomic bias in a CoDA framework is wanting to zero-out a specific set of observations (e.g. of a particular taxon in a particular set of samples). Sometimes this is very easy to do in the melted data frame given by psmelt() or ps_tibble(); but we currently lack an easy way to convert these back into a phyloseq object. I suspect there are other use cases for this workflow of phyloseq -> data frame -> modify abundances -> phyloseq
A use case I sometimes find myself in when analyzing taxonomic bias in a CoDA framework is wanting to zero-out a specific set of observations (e.g. of a particular taxon in a particular set of samples). Sometimes this is very easy to do in the melted data frame given by
psmelt()orps_tibble(); but we currently lack an easy way to convert these back into a phyloseq object. I suspect there are other use cases for this workflow of phyloseq -> data frame -> modify abundances -> phyloseq