metabarlist_to_phyloseq function

[AnneSoBen]

Hi,
I wrote a new function to convert a metabarlist object into a phyloseq object. My idea while writing this function was to directly convert the reads matrix into a phyloseq otu_table object, the samples data frame into a phyloseq sample_data object and part of the motus data frame into a phyloseq tax_table object to group them in a phyloseq object (see this page for phyloseq objects structure: https://joey711.github.io/phyloseq/import-data.html).
This implies that the sample names in the reads matrix (i.e. rownames) should be the the same as in the samples data frame, so that controls were removed and the metabarlist is aggregated at sample level (see example in https://github.com/metabaRfactory/metabaR/blob/phyloseq_functions/R/metabarlist_to_phyloseq.R).
Do you agree with that or would you suggest to make it possible to convert the metabarlist in a phyloseq object at 'pcrs' level? (and thus include information from the pcrs data frame into the phyloseq sample_data object)
AnneSoBen

[lionncle]

Hi,
I agree with you to use samples instead of pcr replicates.
Concerning the sample_data table, you can also consider keeping the controls (positives, pcr, extraction), if it's useful, by using the pcrs and samples table?
With the aggregate_pcrs and subset_metabarlist functions you should be able to develop your function quite easily, I think, and even add options for data aggregation.

Clement