sp_taxa_ID | R Documentation |
Add full taxonomic classification to species ID auto-generated by Phyloseq
sp_taxa_ID(physeq, taxa.col = NA, remove = FALSE, remove.delimiter = "_")
physeq |
Phyloseq object |
taxa.col |
String of taxonomic levels to include in classification. Taxonomic levels must exist in the input phyloseq object. If no input given, defaults to all levels in phyloseq object. |
remove |
TRUE or FALSE. Are there characters that need to be removed after the spID in the taxa rowname to isolate the spID ? If TRUE, spID is extracted (e.g sp1_bacteria_bacteroidetes extracted to sp1) |
remove.delimiter |
Character string that separates sp ID from remaining OTU name characters (e.g sp1_bacteria_bacteroidetes delimiter is "_") |
Returns the phyloseq object with taxonomic classification as part of the taxa name (i.e. phyloseq OTU table rownames now contain taxonomy).
sp_taxa_ID(dat) #Add full taxonomic label to rownames (i.e. sp###_Kingdom_Phylum_Class_Order_Family_Genus) sp_taxa_ID(physeq = dat, taxa.col = c("Family, "Genus)) #Add full taxonomic label to rownames (i.e. sp###_Family_Genus)
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