phyloseq_to_df: Convert phyloseq object to data frame (for exporting).

In vmikk/metagMisc: Miscellaneous functions for metagenomic analysis

Convert phyloseq object to data frame (for exporting).

Description

Convert phyloseq object to data frame (for exporting).

Usage

phyloseq_to_df(
  physeq,
  addtax = T,
  addtot = F,
  addmaxrank = F,
  sorting = "abundance"
)

Arguments

physeq	A phyloseq-class object
addtax	Logical; add taxonomy to the result table (default, TRUE)
addtot	Logical; add total OTU abundance to the resulting table (default, FALSE)
addmaxrank	Logical; add the OTU classification at the lowest annotated taxonomic rank to the resulting table (default, FALSE)
sorting	Reorder OTUs according to their total abundance ("abundance", default) or taxonomy (sorting = "taxonomy"); if reordering is not required use 'sorting = NULL'

Value

Data frame with OTU taxonomy and abundance

See Also

phyloseq-class

Examples

data(GlobalPatterns)
GlobalPatternsDF <- phyloseq_to_df(GlobalPatterns)
str(GlobalPatternsDF)

vmikk/metagMisc documentation built on Feb. 14, 2024, 2:29 a.m.