Mutating Slots of Phyloseq

Mutating Slots of Phyloseq

mutateSampleData(x, ...)

mutateTaxaTable(x, ...)

mutateAbundanceTable(x, ...)

Arguments

x

phyloseq object

...

Arguments that dplyr::mutate can accept

Value

A phyloseq

Details

Mutate different phyloseq slots.

mutateAbundanceTable mutate otu_table. Will also add the new sample to sample_data

mutateTaxaTable mutate tax_table, Add or modify existing columns.

mutateSampleData mutate sample_data. Add columns, modify existing columns.

References

Shetty SA (2020). Utilities for microbiome analytics. https://github.com/RIVM-IIV-Microbiome/biomeUtils

Author

Sudarshan A. Shetty

Examples

library(biomeUtils)
library(dplyr)
data("FuentesIliGutData")
ps_otu <- mutateAbundanceTable(FuentesIliGutData, test = 1:ntaxa(FuentesIliGutData))
ps_tax <- mutateTaxaTable(FuentesIliGutData, test = 1:ntaxa(FuentesIliGutData))
ps_samdat <- mutateSampleData(FuentesIliGutData, test = paste0(ILI, "-test"))