phyloseq-class
Object advancedformat_to_besthit.Rd
Format the phyloseq object to add the best taxonomy in phyloseq object (tax_table and otu_table).
format_to_besthit(x)
x |
|
---|
phyloseq-class
object.
Most commonly it is observed that the taxonomy file has classification until a given taxonomic level.
row.names for both tax_table and otu_table have best hit, until maximun genus level (species classification with short amplicons is a myth)is made available. This code is a
slight modification of the code from ampvis phyloseq-class
.
Here, we directly take the phyloseq object as input and make the necessary formatting.
# NOT RUN { # Example data library(microbiome) library(microbiomeUtilities) library(tibble) data("zackular2014") p0 <- zackular2014 p0.f <- format_to_besthit(p0) # }