met_wo_unk: For each rank from Phylum to Genus, remove all MDM
In ConesaLab/MDM: Complete MDM Network Analysis for 16S rRNA Data

Description Usage Arguments Value Examples

For each rank from Phylum to Genus, remove all MDM from the original OTU table and retain only taxa with known classifications. A reduced OTU table is produced for each rank, retaining only known taxa.

1	met_wo_unk(orig_phylo)

orig_phylo

Phyloseq including all taxa meeting threshold, produced from get_back_res_meeting_min_occ function

Returns list of 7 OTU tables

`table1`	OTU table of all known Kingdom taxa
`table2`	OTU table of all known Phylum taxa
`table3`	OTU table of all known Class taxa
`table4`	OTU table of all known Order taxa
`table5`	OTU table of all known Family taxa
`table6`	OTU table of all known Genus taxa
`table7`	OTU table of all known Species taxa

##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.

## The function is currently defined as
function (orig_phylo)
{
    nodes_list_m = list()
    met_tax_table = phyloseq::tax_table(orig_phylo)
    print(dim(met_tax_table))
    met_tax_table <- as.data.frame(met_tax_table)
    met_tax_table[] <- lapply(met_tax_table, as.character)
    met_tax_table1 <- met_tax_table %>% dplyr::mutate_all(funs(replace(.,
        is.na(.), "Unassigned")))
    rownames(met_tax_table1) = rownames(met_tax_table)
    print(dim(met_tax_table1))
    for (i in 1:length(colnames(met_tax_table1))) {
        print(i)
        unassignedOTUs_MDM <- c("NA", "D_1__uncultured", "D_1__uncultured bacterium",
            "D_1__Unknown Phylum", "D_2__uncultured", "D_2__uncultured bacterium",
            "D_2__Unknown Class", "Ambiguous_taxa", "Unassigned",
            "D_3__uncultured", "D_3__uncultured bacterium", "D_3__Unknown Order",
            "D_4__uncultured", "D_4__uncultured bacterium", "D_4__Unknown Family",
            "D_5__uncultured", "D_5__uncultured bacterium", "D_5__Unknown Genus",
            "D_6__uncultured", "D_6__uncultured bacterium", "D_6__Unknown Species")
        node_a <- met_tax_table1[met_tax_table1[, i] %in% unassignedOTUs_MDM,
            ]
        print(dim(node_a))
        nodes_list_m[[i]] = node_a
    }
    final_otus = phyloseq::otu_table(orig_phylo)
    print(dim(final_otus))
    wo_unk_otus_at_tax_level_l = list()
    for (t in 1:length(nodes_list_m)) {
        print(t)
        unk_otus_at_tax_level <- final_otus[!rownames(final_otus) %in%
            rownames(nodes_list_m[[t]]), ]
        print(dim(unk_otus_at_tax_level))
        wo_unk_otus_at_tax_level_l[[t]] = unk_otus_at_tax_level
    }
    names(wo_unk_otus_at_tax_level_l) = colnames(tax_table(orig_phylo))
    return(wo_unk_otus_at_tax_level_l)
  }