View source: R/format_to_besthit.R
format_to_besthit | 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, prefix = NULL)
x |
|
prefix |
Prefered prefix e.g. OTU-d__denovo161:Roseburia or ASV-d__denovo161:Roseburia |
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(dplyr) data("zackular2014") p0 <- zackular2014 p0.f <- format_to_besthit(p0, prefix = "OTU-") ## End(Not run)
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