format_phyloseq: Formatting the Phyloseq Object

In microsud/microbiomeutilities-shiny: microbiomeutilities: An R package with utility functions for the microbiome R package

Description

Format the phyloseq object to add the best taxonomy in phyloseq object (tax_table).

Usage

format_phyloseq(x)

Arguments

x	phyloseq-class object

Details

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.

Value

phyloseq-class object.

Examples

## Not run: 
  # Example data
    library(microbiome)
    library(microbiomeUtilities)
    data("biogeogut")
    p0 <- biogeogut
    p0.f <- format_phyloseq(biogeogut)
          
## End(Not run)

microsud/microbiomeutilities-shiny documentation built on May 7, 2019, 9:38 a.m.