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
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