create_taxmap: Get Taxmap Object

In vallenderlab/MicrobiomeR: Analyze Microbiome Data

Description

A function that handles the conversion of objects to Taxmap (taxa::taxmap) objects.

Usage

create_taxmap(obj)

Arguments

obj

An object that contains the data being analyzed. Can be one of the following: Phyloseq Object An object generated from the phyloseq package. Taxmap Object An object generated from the metacoder or taxa package. RData file An RData file generated from the base::save function. Can have an extension of .RData or .rda.

Details

This function is used to convert data to metacoder/taxmap objects for microbiome analysis. This function is used at the beginning of every other function to support multiple types of input for the obj parameter in those functions.

Value

The output generated is a taxa::taxmap object.

See Also

parse_phyloseq

fileutils

Other Data Importers: create_phyloseq

Examples

## Not run: 
if(interactive()){
 library(MicrobiomeR)
 phy_obj <- MicrobiomeR::phyloseq_silva_2
 mc_obj <- create_taxmap(phy_obj)
 }

## End(Not run)

vallenderlab/MicrobiomeR documentation built on Aug. 30, 2019, 11:24 p.m.