phy_to_ldf: Convert phyloseq object to long data format

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

Description

Faster alternative to psmelt function from phyloseq-class object.

Usage

phy_to_ldf(x, transform.counts)

Arguments

x	phyloseq-class object
transform.counts	Data transform to be used in plotting (but not in sample/taxon ordering). The options are 'Z-OTU', 'Z-Sample', 'log10' and 'compositional'. See the transform function.

Value

A data frame in long format with appropriate transfomation if requested.

Examples

## Not run: 
  # Example data
    library(microbiomeutilities)
    data("biogeogut")
    pseq <- biogeogut
    pseq_df <- phy_to_ldf(pseq, transform.counts = NULL)

          
## End(Not run)

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