| format_to_besthit {microbiomeutilities} | R Documentation |
phyloseq-class Object advancedFormat the phyloseq object to add the best taxonomy in phyloseq object (tax_table and otu_table).
format_to_besthit(x)
x |
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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.
phyloseq-class object.
## Not run:
# Example data
library(microbiome)
library(microbiomeUtilities)
library(tibble)
data("zackular2014")
p0 <- zackular2014
p0.f <- format_to_besthit(p0)
## End(Not run)