phyloseq-class
Objectformat_phyloseq.Rd
Format the phyloseq object to add the best taxonomy in phyloseq object (tax_table).
format_phyloseq(x)
x |
|
---|
phyloseq-class
object.
Most commonly it is observed that the taxonomy file has classification until a given taxonomic level.
Hence, to avoid loss of OTU information while using the function tax_glom() for merging at a specific taxonomic level.
we will fill the empty cells with the maximum classification available along with the OTU number. 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 { library(microbiome) library(microbiomeutilities) data("zackular2014") p0 <- zackular2014 p0.f <- format_phyloseq(p0) head(tax_table(p0.f)) # }