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

    #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)

[Package microbiome version 1.12.0 Index]