import ASV sequences rep_fasta using phyloseq2meco

[fconstancias]

Dear @ChiLiubio,

Thanks for this game changing R package.
I am trying to import a phyloseq object using file2meco::phyloseq2meco.

My initial phyloseq object contains ASV sequences refseq() but it is missing from the microtable-class object generated using microtable-class object file2meco::phyloseq2meco.

physeq
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 64 taxa and 116 samples ]
sample_data() Sample Data:       [ 116 samples by 26 sample variables ]
tax_table()   Taxonomy Table:    [ 64 taxa by 7 taxonomic ranks ]
phy_tree()    Phylogenetic Tree: [ 64 tips and 63 internal nodes ]
refseq()      DNAStringSet:      [ 64 reference sequences ]

 physeq %>%
    file2meco::phyloseq2meco(.) -> data

data
microtable-class object:
sample_table have 116 rows and 26 columns
otu_table have 64 rows and 116 columns
tax_table have 64 rows and 7 columns
phylo_tree have 64 tips

Is it expected? How ot fix this?

Thanks

[ChiLiubio]

Hi @fconstancias

Thanks very much! I find I ignored the sequences conversion between phylsoeq and microtable. I have added this and updated file2meco package in github. It is ok now in my test. If necessary, please reinstall the package from github and try again.

Best,
Chi