read_mothur2phyloseq {microbiome}R Documentation

Read Mothur Output into a Phyloseq Object

Description

Read mothur shared and consensus taxonomy files into a phyloseq-class object.

Usage

read_mothur2phyloseq(shared.file, consensus.taxonomy.file,
  mapping.file = NULL)

Arguments

shared.file

A shared file produced by mothur. Identified from the .shared extension

consensus.taxonomy.file

Consensus taxonomy file produced by mothur. Identified from with the .taxonomy extension. See http://www.mothur.org/wiki/ConTaxonomy_file.

mapping.file

Metadata/mapping file with .csv extension

Details

Mothur shared and consensus taxonomy files will be converted to phyloseq-class.

Value

phyloseq-class object.

Author(s)

Sudarshan A. Shetty sudarshanshetty9@gmail.com

Examples

## Not run: 

otu.file <- system.file(
"extdata/Baxter_FITs_Microbiome_2016_fit.final.tx.1.subsample.shared",
   package='microbiome')

tax.file <- system.file(
"extdata/Baxter_FITs_Microbiome_2016_fit.final.tx.1.cons.taxonomy",
   package='microbiome')

meta.file <- system.file(
"extdata/Baxter_FITs_Microbiome_2016_mapping.csv",
   package='microbiome')

p0 <- read_mothur2phyloseq(
       shared.file=otu.file,
       consensus.taxonomy.file=tax.file,
       mapping.file=meta.file)

## End(Not run)

[Package microbiome version 1.0.2 Index]