| format_phyloseq {microbiomeutilities} | R Documentation |
phyloseq-class ObjectFormat the phyloseq object to add the best taxonomy in phyloseq object (tax_table).
format_phyloseq(x)
x |
|
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.
phyloseq-class object.
## Not run:
library(microbiome)
library(microbiomeutilities)
data("zackular2014")
p0 <- zackular2014
p0.f <- format_phyloseq(p0)
head(tax_table(p0.f))
## End(Not run)